Typing of S. epidermidis samples (MD P.B.)

Characterization_of_the_virulence_agr_typing_and_antimicrobial_resistance_profile_of_Staphylococcus_aureus_strains.pdf

1. Goal of data analyses

   S epidermidis genomes
       1. Assemble closed genomes from HDRNA 1, 3, 6, 7, 8, 12, 16, 17, 19, 20 (short read + long read)
           TODO: make a table similar to the paper Characterization of the virulence, agr typing and antimicrobial resistance profile of Staphylococcus aureus strains isolated from food handlers in Brazil Table 2, and draw a tree+heatmaps Figure!
           Based on closed genomes:
           - Sequence type,
           - goeBURST analysis (-->performed is geoBURST TLV-Analysis, see point 2),
           - SCCmec type (https://www.sccmec.org/index.php/en/method-to-identify-sccmmcc-smn-en/review-smn-en) https://cge.cbs.dtu.dk/services/SCCmecFinder/
             SCCmec typing: https://www.genomicepidemiology.org/ --> https://cge.food.dtu.dk/services/SCCmecFinder/
               SCCmecFinder 1.2
               SCCmecFinder identifies SCCmec elements in sequenced S. aureus isolates. The SCCmec element is the defining feature of methicillin-resistant S. aureus isolates, and encodes the single determinant for methicillin resistant, the mecA gene.
               IMPORTANT! SCCmec typing is only available for SCCmec type I-XI and subtyping is currently only available for SCCmec type IV and V
               IMPORTANT! mec gene complex C1 and C2 might produce errors.
   
           - agr typing: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187671/ (see point 3)
   
           - presence phage HH1, SPbeta-like phage, phage related island [referring to A´s paper] (see point 5),
   
           - absence/presence matrix for selected genes [see attached ppt, see results in Gene_List.pptx] (see point 6)
             gyrB,  fumC, , icd, apsS,
             sigB, sarA, , , ,
             ,  , sdrG(-17), sdrH, ebh, ebp (ebpS), ,
             , , dltA, , lipA,
             , , , , , ,
             --> draw a circle heatmaps including all data with a very big figure and table.
   
       2. according to assembled genomes describe within host diversity per patient (i.e. compare isolates 2 – 10 to isolate 1).
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_01_K01_conservative_23197.current.gb HDRNA_01_K01_CP133676.xlsx
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_03_K01_bold_bandage_26831.current.gb HDRNA_03_K01_CP133677.xlsx
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_06_K01_conservative_27645.current.gb HDRNA_06_K01_CP133678-CP133679.xlsx
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_07_K01_conservative_27169.current.gb HDRNA_07_K01_CP133680-CP133681.xlsx
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_08_K01_conservative_32455.current.gb HDRNA_08_K01_CP133682-CP133683.xlsx
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_12_K01_bold_37467.current.gb HDRNA_12_K01_CP133684-CP133687.xlsx
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_16_K01_conservative_37834.current.gb HDRNA_16_K01_CP133688-CP133692.xlsx
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_17_K01_conservative_37288.current.gb HDRNA_17_K01_CP133693-CP133695.xlsx
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_19_K01_bold_37377.current.gb HDRNA_19_K01_CP133696-CP133699.xlsx
           python3 /home/jhuang/Scripts/gb_to_excel.py ./gbks/HDRNA_20_K01_conservative_43457.current.gb HDRNA_01_K01_CP133700-CP133701.xlsx
   
           * SNP INDEL: snippy+spandx --> get the complete list of SNP+INDEL for each isolate group!!! (see point 4)
   
           * gene absence/presence:
           # A: prepare prokka_HDRNA_01 .. prokka_HDRNA_20 from prokka_remaining
   
           # B:         #https://github.com/jorvis/biocode/blob/master/gff/convert_genbank_to_gff3.py
           sudo apt-get install -y python3 python3-pip zlib1g-dev libblas-dev liblapack-dev libxml2-dev
           pip3 install biocode
           convert_genbank_to_gff3.py -i HDRNA_01_K01_conservative_23197.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_01/HDRNA_01_K01.gff --with_fasta
           convert_genbank_to_gff3.py -i HDRNA_03_K01_bold_bandage_26831.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_03/HDRNA_03_K01.gff --with_fasta
           convert_genbank_to_gff3.py -i HDRNA_06_K01_conservative_27645.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_06/HDRNA_06_K01.gff --with_fasta
           convert_genbank_to_gff3.py -i HDRNA_07_K01_conservative_27169.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_07/HDRNA_07_K01.gff --with_fasta
           convert_genbank_to_gff3.py -i HDRNA_08_K01_conservative_32455.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_08/HDRNA_08_K01.gff --with_fasta
           convert_genbank_to_gff3.py -i HDRNA_12_K01_bold_37467.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_12/HDRNA_12_K01.gff --with_fasta
           convert_genbank_to_gff3.py -i HDRNA_16_K01_conservative_37834.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_16/HDRNA_16_K01.gff --with_fasta
           convert_genbank_to_gff3.py -i HDRNA_17_K01_conservative_37288.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_17/HDRNA_17_K01.gff --with_fasta
           convert_genbank_to_gff3.py -i HDRNA_19_K01_bold_37377.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_19/HDRNA_19_K01.gff --with_fasta
           convert_genbank_to_gff3.py -i HDRNA_20_K01_conservative_43457.current.gb -o ~/DATA/Data_PaulBongarts_S.epidermidis_HDRNA/Data_Holger_S.epidermidis_short/prokka_HDRNA_20/HDRNA_20_K01.gff --with_fasta
   
           # C: check gff.files if containing the repeated gene names using check_duplicate_cds.py, remove manually, recheck the removed one.
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_01_K01.gff
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_03_K01.gff
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_06_K01.gff
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_07_K01.gff
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_08_K01.gff
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_12_K01.gff
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_16_K01.gff
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_17_K01.gff
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_19_K01.gff
           python3 ~/Scripts/check_duplicate_cds.py HDRNA_20_K01.gff
               Found duplicates for the following CDS IDs:
               RE430_09810.mRNA.0.CDS.1
               RE430_08580.mRNA.0.CDS.1
               RE430_09730.mRNA.0.CDS.1
               RGR13_00575.mRNA.0.CDS.1
               RGR10_09570.mRNA.0.CDS.1
               RGR06_10025.mRNA.0.CDS.1
               RGR06_12305.mRNA.0.CDS.1
               #xxxx
               RGR12_09490.mRNA.0.CDS.1
               RGR12_00425.mRNA.0.CDS.1
               RGR12_11570.mRNA.0.CDS.1
               RGR09_12270.mRNA.0.CDS.1
               RGR09_09635.mRNA.0.CDS.1
               RGR09_01280.mRNA.0.CDS.1
               RGR08_01845.mRNA.0.CDS.1
               RGR08_13135.mRNA.0.CDS.1
               RGR08_10360.mRNA.0.CDS.1
               RGR08_09845.mRNA.0.CDS.1
               RGR14_00635.mRNA.0.CDS.1
               RGR14_00355.mRNA.0.CDS.1
               RGR14_09870.mRNA.0.CDS.1
               RGR14_01550.mRNA.0.CDS.1
   
               RGR07_09075.mRNA.0.CDS.1
               RGR07_00190.mRNA.0.CDS.1
               RGR07_11485.mRNA.0.CDS.1
               RGR07_00090.mRNA.0.CDS.1
               RGR07_11545.mRNA.0.CDS.1
               RGR07_01915.mRNA.0.CDS.1
               RGR11_01280.mRNA.0.CDS.1
               RGR11_09700.mRNA.0.CDS.1
   
           rsync -a -P prokka_HDRNA_01/HDRNA_01_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_01/
           rsync -a -P prokka_HDRNA_03/HDRNA_03_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_03/
           rsync -a -P prokka_HDRNA_06/HDRNA_06_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_06/
           rsync -a -P prokka_HDRNA_07/HDRNA_07_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_07/
           rsync -a -P prokka_HDRNA_08/HDRNA_08_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_08/
           rsync -a -P prokka_HDRNA_12/HDRNA_12_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_12/
           rsync -a -P prokka_HDRNA_16/HDRNA_16_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_16/
           rsync -a -P prokka_HDRNA_17/HDRNA_17_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_17/
           rsync -a -P prokka_HDRNA_19/HDRNA_19_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_19/
           rsync -a -P prokka_HDRNA_20/HDRNA_20_K01.gff jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_20/
   
           cd prokka_HDRNA_01
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_01_K01.gff ./HDRNA_01_K02/HDRNA_01_K02.gff ./HDRNA_01_K03/HDRNA_01_K03.gff ./HDRNA_01_K04/HDRNA_01_K04.gff ./HDRNA_01_K05/HDRNA_01_K05.gff ./HDRNA_01_K06/HDRNA_01_K06.gff ./HDRNA_01_K07/HDRNA_01_K07.gff ./HDRNA_01_K08/HDRNA_01_K08.gff ./HDRNA_01_K09/HDRNA_01_K09.gff ./HDRNA_01_K10/HDRNA_01_K10.gff
           cd ../prokka_HDRNA_03
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_03_K01.gff ./HDRNA_03_K02/HDRNA_03_K02.gff ./HDRNA_03_K03/HDRNA_03_K03.gff ./HDRNA_03_K04/HDRNA_03_K04.gff ./HDRNA_03_K05/HDRNA_03_K05.gff ./HDRNA_03_K06/HDRNA_03_K06.gff ./HDRNA_03_K07/HDRNA_03_K07.gff ./HDRNA_03_K08/HDRNA_03_K08.gff ./HDRNA_03_K09/HDRNA_03_K09.gff ./HDRNA_03_K10/HDRNA_03_K10.gff
           cd ../prokka_HDRNA_06
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_06_K01.gff ./HDRNA_06_K02/HDRNA_06_K02.gff ./HDRNA_06_K03/HDRNA_06_K03.gff ./HDRNA_06_K04/HDRNA_06_K04.gff ./HDRNA_06_K05/HDRNA_06_K05.gff ./HDRNA_06_K06/HDRNA_06_K06.gff ./HDRNA_06_K07/HDRNA_06_K07.gff ./HDRNA_06_K08/HDRNA_06_K08.gff ./HDRNA_06_K09/HDRNA_06_K09.gff ./HDRNA_06_K10/HDRNA_06_K10.gff
           cd ../prokka_HDRNA_07
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_07_K01.gff ./HDRNA_07_K02/HDRNA_07_K02.gff ./HDRNA_07_K03/HDRNA_07_K03.gff ./HDRNA_07_K04/HDRNA_07_K04.gff ./HDRNA_07_K05/HDRNA_07_K05.gff ./HDRNA_07_K06/HDRNA_07_K06.gff ./HDRNA_07_K07/HDRNA_07_K07.gff ./HDRNA_07_K08/HDRNA_07_K08.gff ./HDRNA_07_K09/HDRNA_07_K09.gff ./HDRNA_07_K10/HDRNA_07_K10.gff
           cd ../prokka_HDRNA_08
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_08_K01.gff ./HDRNA_08_K02/HDRNA_08_K02.gff ./HDRNA_08_K03/HDRNA_08_K03.gff ./HDRNA_08_K04/HDRNA_08_K04.gff ./HDRNA_08_K05/HDRNA_08_K05.gff ./HDRNA_08_K06/HDRNA_08_K06.gff ./HDRNA_08_K07/HDRNA_08_K07.gff ./HDRNA_08_K08/HDRNA_08_K08.gff ./HDRNA_08_K09/HDRNA_08_K09.gff ./HDRNA_08_K10/HDRNA_08_K10.gff
           cd ../prokka_HDRNA_12
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_12_K01.gff ./HDRNA_12_K02/HDRNA_12_K02.gff ./HDRNA_12_K03/HDRNA_12_K03.gff ./HDRNA_12_K04/HDRNA_12_K04.gff ./HDRNA_12_K05/HDRNA_12_K05.gff ./HDRNA_12_K06/HDRNA_12_K06.gff ./HDRNA_12_K07/HDRNA_12_K07.gff ./HDRNA_12_K08/HDRNA_12_K08.gff ./HDRNA_12_K09/HDRNA_12_K09.gff ./HDRNA_12_K10/HDRNA_12_K10.gff
           cd ../prokka_HDRNA_16
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_16_K01.gff ./HDRNA_16_K02/HDRNA_16_K02.gff ./HDRNA_16_K03/HDRNA_16_K03.gff ./HDRNA_16_K04/HDRNA_16_K04.gff ./HDRNA_16_K05/HDRNA_16_K05.gff ./HDRNA_16_K06/HDRNA_16_K06.gff ./HDRNA_16_K07/HDRNA_16_K07.gff ./HDRNA_16_K08/HDRNA_16_K08.gff ./HDRNA_16_K09/HDRNA_16_K09.gff ./HDRNA_16_K10/HDRNA_16_K10.gff
           cd ../prokka_HDRNA_17
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_17_K01.gff ./HDRNA_17_K02/HDRNA_17_K02.gff ./HDRNA_17_K03/HDRNA_17_K03.gff ./HDRNA_17_K04/HDRNA_17_K04.gff ./HDRNA_17_K05/HDRNA_17_K05.gff ./HDRNA_17_K06/HDRNA_17_K06.gff ./HDRNA_17_K07/HDRNA_17_K07.gff ./HDRNA_17_K08/HDRNA_17_K08.gff ./HDRNA_17_K09/HDRNA_17_K09.gff ./HDRNA_17_K10/HDRNA_17_K10.gff
           cd ../prokka_HDRNA_19
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_19_K01.gff ./HDRNA_19_K02/HDRNA_19_K02.gff ./HDRNA_19_K03/HDRNA_19_K03.gff ./HDRNA_19_K04/HDRNA_19_K04.gff ./HDRNA_19_K05/HDRNA_19_K05.gff ./HDRNA_19_K06/HDRNA_19_K06.gff ./HDRNA_19_K07/HDRNA_19_K07.gff ./HDRNA_19_K08/HDRNA_19_K08.gff ./HDRNA_19_K09/HDRNA_19_K09.gff ./HDRNA_19_K10/HDRNA_19_K10.gff
           cd ../prokka_HDRNA_20
           roary -p 5 -f ./roary -i 95 -cd 99 -s -e -n -v ./HDRNA_20_K01.gff ./HDRNA_20_K02/HDRNA_20_K02.gff ./HDRNA_20_K03/HDRNA_20_K03.gff ./HDRNA_20_K04/HDRNA_20_K04.gff ./HDRNA_20_K05/HDRNA_20_K05.gff ./HDRNA_20_K06/HDRNA_20_K06.gff ./HDRNA_20_K07/HDRNA_20_K07.gff ./HDRNA_20_K08/HDRNA_20_K08.gff ./HDRNA_20_K09/HDRNA_20_K09.gff
           cd ..
   
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_01/roary prokka_HDRNA_01
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_03/roary prokka_HDRNA_03
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_06/roary prokka_HDRNA_06
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_07/roary prokka_HDRNA_07
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_08/roary prokka_HDRNA_08
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_12/roary prokka_HDRNA_12
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_16/roary prokka_HDRNA_16
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_17/roary prokka_HDRNA_17
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_19/roary prokka_HDRNA_19
           rsync -a -P jhuang@hamm:~/DATA/Data_Holger_S.epidermidis_short/prokka_HDRNA_20/roary prokka_HDRNA_20
   
           cp prokka_HDRNA_01/roary/gene_presence_absence.csv gene_presence_absence__HDRNA_01.csv
           cp prokka_HDRNA_03/roary/gene_presence_absence.csv gene_presence_absence_HDRNA_03.csv
           cp prokka_HDRNA_06/roary/gene_presence_absence.csv gene_presence_absence_HDRNA_06.csv
           cp prokka_HDRNA_07/roary/gene_presence_absence.csv gene_presence_absence_HDRNA_07.csv
           cp prokka_HDRNA_08/roary/gene_presence_absence.csv gene_presence_absence_HDRNA_08.csv
           cp prokka_HDRNA_12/roary/gene_presence_absence.csv gene_presence_absence_HDRNA_12.csv
           cp prokka_HDRNA_16/roary/gene_presence_absence.csv gene_presence_absence_HDRNA_16.csv
           cp prokka_HDRNA_17/roary/gene_presence_absence.csv gene_presence_absence_HDRNA_17.csv
           cp prokka_HDRNA_19/roary/gene_presence_absence.csv gene_presence_absence_HDRNA_19.csv
           cp prokka_HDRNA_20/roary/gene_presence_absence.csv gene_presence_absence_HDRNA_20.csv
   
           #Wenn man will open the files mit libreoffice, needs "," --> "|"; "\n"-->\n; the first and last " in the text; in the kate, then open file with libreoffice with delimiter '|'.
   
           sed -i 's/\.mRNA\.0\.CDS\.1//g' gene_presence_absence__HDRNA_01.csv
   
           group_10||Y_phosphoryl: pyrimidine-nucleoside phosphorylase|10|11|1.11|1|416||||362|1301|1165|RE430_03860|HDRNA_01_K02_02111|HDRNA_01_K03_02181|HDRNA_01_K04_02110|HDRNA_01_K05_02181|HDRNA_01_K06_02156|HDRNA_01_K07_02196     HDRNA_01_K07_02197|HDRNA_01_K08_01754|HDRNA_01_K09_02226|HDRNA_01_K10_02107
   
           group_10||Y_phosphoryl: pyrimidine-nucleoside phosphorylase|10|11|1.11|1|416||||362|1301|1165|RE430_03860.mRNA.0.CDS.1|HDRNA_01_K02_02111|HDRNA_01_K03_02181|HDRNA_01_K04_02110|HDRNA_01_K05_02181|HDRNA_01_K06_02156|HDRNA_01_K07_02196    HDRNA_01_K07_02197|HDRNA_01_K08_01754|HDRNA_01_K09_02226|HDRNA_01_K10_02107
   
           for file in gene_presence_absence_HDRNA_*; do
               sed -i 's/\.mRNA\.0\.CDS\.1//g' "$file"
           done
   
           ~/Tools/csv2xls-0.4/csv_to_xls.py gene_presence_absence__HDRNA_01.csv gene_presence_absence_HDRNA_03.csv gene_presence_absence_HDRNA_06.csv gene_presence_absence_HDRNA_07.csv gene_presence_absence_HDRNA_08.csv gene_presence_absence_HDRNA_12.csv gene_presence_absence_HDRNA_16.csv gene_presence_absence_HDRNA_17.csv gene_presence_absence_HDRNA_19.csv gene_presence_absence_HDRNA_20.csv -d'|' -o gene_presence_absence.xls
   
           * genomic rearrangements (e.g. SCCmec deletions, ACME deletions, agr insertions)
             TODOs using Easyfig!
             #Staphylococcal Cassette Chromosome mec
             #arginine catabolic mobile element (ACME)
   
           #Prevalence and genetic diversity of arginine catabolic mobile element (ACME) in clinical isolates of coagulase-negative staphylococci: identification of ACME type I variants in Staphylococcus epidermidis.
           Fig. 1. A schematic drawing of genetic structures of ACME (a region from the arc to opp3 cluster, or corresponding genetic components) among the three DI subtypes (DI.1, DI.2, and DI.3: strains CNS266, CNS115, and CNS149, respectively), type I (strain USA300-FPR3757, accession number CP000255), type II (strain ATCC12228, accession number AE015929) and type DII (strain M08/0126, accession number FR753166). Putative ORFs of genes are represented by arrows colored with green (arc cluster), red (opp3 cluster), blue (a region between the arc and opp3 clusters in ACME I), or dark blue (genes in ACME II). The regions in light pink including the arc cluster indicate genetically identical areas to both ATCC12228 and USA300-FPR3757. The regions with light blue are identical to only ATCC12228, while those with light orange to USA300-FPR3757. White space regions between argR and SAUSA300_0072 show no sequence homology either to ATCC12228 or to USA300_FPR3757; however, these regions show 91–99% nucleotide identity among the three ACME subtypes. Regions colored with dark orange in the three ACME DI subtypes show=98% nucleotide sequence identity to each other. Regions colored with grey (type DI.1), purple or cyan (type DI.3) do not show high nucleotide identity (<98%) to cognate genes in other ACME types (Table S2.2). Positions of primers used for PCR profile (Tables 1 and 4) are shown with arrowheads under ACME I sequence. Collapse
   
             #Smash++: https://academic.oup.com/gigascience/article/9/5/giaa048/5841055
             #https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7597632/
   
           Artemis Comparison Tool (ACT): Allows for the visual comparison of genomes and can be used to investigate the presence or absence of genomic regions (such as SCCmec or ACME) and other structural variations.
           #https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009304
           #https://journals.plos.org/plospathogens/article/figure?id=10.1371/journal.ppat.1009304.g010
   
           The image you uploaded appears to be a schematic representation of genomic rearrangements, typically found in scientific publications or reports. These kinds of images are often created using bioinformatics visualization tools or general graphic design software. While it's not possible to determine the exact software used to create this specific image without more context, I can suggest several tools commonly used for such purposes:
   
       3. Epidome: (using R?) Create bar plot showing ST distribution in noses from patients HDRNA 1, 3, 6,   --> 7, 8, 12, 16, 17, 19, 20 <--
       (Easy using R) Create table showing presence / absence of STs / per patient
       NOTE: Epidome data have not been processed due to potential missing of the data; At first sending the results without Epidome results, ask again where is the epidome data for the 10 patients?
   

2. generate goeBURST

   5,1,1,1,2,2,1,1
   87,7,1,1,2,2,1,1
   35,2,1,2,2,4,1,1
   69,1,18,6,2,2,1,1
   
   23,7,1,2,1,3,3,1
   224,19,16,19,6,3,19,10
   640,28,3,13,5,8,9,11
   
   '-',1,13,2,1,2,1,29
   
   in goeBURST-1.2.1.jar, I have gelesen "Edge level to define group SLV DLV TLV". Wie kann ich generate SLV, DLV and TLV files?
   
   The input you've provided seems to represent allelic profiles or sequence types (STs) used in microbial typing, particularly in methods like Multilocus Sequence Typing (MLST). When you input these profiles into software like goeBURST (implemented in a tool like PHYLOViZ), the software uses these profiles to construct a phylogenetic network. The network shows relationships between different strains or isolates based on their allelic similarity.
   
   In goeBURST, groups are defined based on their allelic differences:
   
   SLV (Single-Locus Variants): Strains or STs differing by only one locus.
   DLV (Double-Locus Variants): Strains or STs differing by two loci.
   TLV (Triple-Locus Variants): Strains or STs differing by three loci.
   

3. agr typing S. epidermidis

   > Comparison of the amino acid sequences of a region of the N-terminus of AgrC (A), and AgrB (B) of S. epidermidis (S.e.), S. aureus (S.a.) and S. lugdunensis (S.l.).
   > https://academic.oup.com/femsle/article/163/1/1/625220: Cloning and characterization of an accessory gene regulator (agr)-like locus from Staphylococcus epidermidis
   
   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5064449/
   https://brieflands.com/articles/archcid-62833#4.-Results
   
   https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1282
   Staphylococcus epidermidis Agr Operon
   https://academic.oup.com/femspd/article/51/1/220/501159
   
   #pAgr (S. epidermidis agr operon promoter)
   https://parts.igem.org/Part:BBa_K212003#
   
   - An overall homology of 68% was found between the agr locus from S. epidermidis and S. aureus.
   - The agr locus from S. epidermidis was organized similar to those from S. aureus and S. lugdunensis.
   - The putative RNAII molecule contains four open reading frames, agrA, B, C and D. AgrA was a response regulator.
   - AgrB showed homology with transducer and translocase molecules.
   - AgrC is expected to act as a histidine protein kinase in which a leucine zipper is present.
   - AgrD is presumably processed into an autoinducer peptide.
   
   - For a long time, Staphylococcus epidermidis, as a member of the coagulase-negative staphylococci, was considered as part of the physiological skin flora of the human being with no pathogenic significance.
   - Today, we know that S. epidermidis is one of the most prevalent causes for implant-associated and nosocomial infections.
   - We performed pheno- and genotypic analysis (ica, IS256, SCCmec types, agr groups) of biofilm formation in 200 isolates.
   - Fifty percent were genetically ica-positive and produced biofilm.
   - Among all studied isolates, agr II and III and SCCmec type I were the most prevalent, whereas within the selected multi-resistant isolates (29%), agr I and III and SCCmec type II dominated.
   - SCCmec type I and mecA-negative S. epidermidis isolates were associated with agr II.
   - The majority of the blood culture and biopsy isolates were assigned to agr III and SCCmec type I, whereas agr II was predominantly detected in mecA-negative S. epidermidis isolated from catheter and implant materials.
   - MLST analysis revealed the major clonal lineages of ST2, ST5, ST10, and ST242 (total 13 STs).
   - ST2 isolates from blood cultures were icaA/D-positive and harbored SCCmec types II and III and IS256, whereas the icaA/D- and IS256-positive ST23 isolates were assigned to SCCmec types I and IV.
   
   # -- OPTION 1 using AgrVATE gp1-4-operon_ref.fasta (failed since the database contains only agr from Staphylococcus aureus) --
   
   > Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations
   
   makeblastdb -in HDRNA_K01.fna -dbtype nucl
   -perc_identity 90 -qcov_hsp_perc 90
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query /home/jhuang/Tools/AgrVATE/agrvate_databases/references/gp1-4-operon_ref.fasta -evalue 0.1 -num_threads 15 -outfmt "6 sseqid qseqid evalue pident sstart send" -strand both -max_target_seqs 1
   
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query gp1-4-operon_ref.fasta -evalue 0.1 -num_threads 15 -outfmt "6 sseqid qseqid evalue pident sstart send" -strand both > HDRNA_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query /home/jhuang/Tools/AgrVATE/agrvate_databases/references/gp1-4-operon_ref.fasta -evalue 0.1 -num_threads 15 -outfmt "6 sseqid qseqid evalue pident sstart send" -strand both > HDRNA_03.blastn
   
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query /home/jhuang/Tools/AgrVATE/agrvate_databases/gp1234_all_motifs.fna -evalue 0.1 -num_threads 15 -outfmt "6 sseqid qseqid evalue pident sstart send" -strand both > HDRNA_01_.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query /home/jhuang/Tools/AgrVATE/agrvate_databases/gp1234_all_motifs.fna -evalue 0.1 -num_threads 15 -outfmt "6 sseqid qseqid evalue pident sstart send" -strand both > HDRNA_03_.blastn
   
   # -- OPTION 2 using agr-1-3_Se.fasta (failed!) --
   
   > High Genetic Variablity of the agr Locus in Staphylococcus Species
   
   >gi|3320006|emb|Z49220.1| Staphylococcus epidermidis hld and agr[A,B,C,D] genes
   
   >gi|18251022|gb|AF346724.1| Staphylococcus epidermidis strain N910160 AgrB (agrB) gene, partial cds; AgrD (agrD) gene, complete cds; and AgrC (agrC) gene, partial cds
   
   >gi|18251026|gb|AF346725.1| Staphylococcus epidermidis strain N910191 AgrB (agrB) gene, partial cds; AgrD (agrD) gene, complete cds; and AgrC (agrC) gene, partial cds
   
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query agr-1-3_Se.fasta -evalue 0.1 -num_threads 15 -outfmt 6 -strand both > HDRNA_01__.blastn
   
   # -- OPTION 3 using agrD_I-III.fasta (successful!) --
   
   > Staphylococcus epidermidis agr Quorum-Sensing System: Signal Identification, Cross Talk, and Importance in Colonization
   
   > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187671/
   
   > https://www.researchgate.net/publication/264391883
   
   tblastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_01.tblastn
   tblastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_03.tblastn
   tblastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_06.tblastn
   tblastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_07.tblastn
   tblastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_08.tblastn
   tblastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_12.tblastn
   tblastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_16.tblastn
   tblastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_17.tblastn
   tblastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_19.tblastn
   tblastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna  -query agrD_I-III.fasta -evalue 0.1 -num_threads 15  > HDRNA_20.tblastn
   
   II?
   II
   I
   II
   I
   
   II
   II
   II
   III
   II
   
   >AgrD_I
   MENIFNLFIKFFTTILEFIGTVAGDSVCASYFDEPEVPEELTKLYE
   >AgrD_II
   MNLLGGLLLKIFSNFMAVIGNASKYNPCSNYLDEPQVPEELTKLDE
   >AgrD_III
   MNLLGGLLLKLFSNFMAVIGNAAKYNPCASYLDEPQVPEELTKLDE
   

4. Variant (SNP+INDEL) calling

   Input files:
       HDRNA_01_K01_conservative_23197.current.gb
   
       HDRNA_01_K01_conservative_23197.current.gb:LOCUS       CP133676             2502964 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_03_K01_bold_bandage_26831.current.gb:LOCUS       CP133677             2590275 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_06_K01_conservative_27645.current.gb:LOCUS       CP133678             2465260 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_06_K01_conservative_27645.current.gb:LOCUS       CP133679               19348 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_07_K01_conservative_27169.current.gb:LOCUS       CP133680             2544074 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_07_K01_conservative_27169.current.gb:LOCUS       CP133681                2241 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_08_K01_conservative_32455.current.gb:LOCUS       CP133682             2425353 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_08_K01_conservative_32455.current.gb:LOCUS       CP133683                6358 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_12_K01_bold_37467.current.gb:LOCUS       CP133684             2490139 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_12_K01_bold_37467.current.gb:LOCUS       CP133685               43849 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_12_K01_bold_37467.current.gb:LOCUS       CP133686                6642 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_12_K01_bold_37467.current.gb:LOCUS       CP133687                2241 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_16_K01_conservative_37834.current.gb:LOCUS       CP133688             2626440 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_16_K01_conservative_37834.current.gb:LOCUS       CP133689               24906 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_16_K01_conservative_37834.current.gb:LOCUS       CP133690               20828 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_16_K01_conservative_37834.current.gb:LOCUS       CP133691                4567 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_16_K01_conservative_37834.current.gb:LOCUS       CP133692                2242 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_17_K01_conservative_37288.current.gb:LOCUS       CP133693             2503072 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_17_K01_conservative_37288.current.gb:LOCUS       CP133694               29861 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_17_K01_conservative_37288.current.gb:LOCUS       CP133695                4439 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_19_K01_bold_37377.current.gb:LOCUS       CP133696             2362062 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_19_K01_bold_37377.current.gb:LOCUS       CP133697               55320 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_19_K01_bold_37377.current.gb:LOCUS       CP133698               46464 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_19_K01_bold_37377.current.gb:LOCUS       CP133699               11827 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_20_K01_conservative_43457.current.gb:LOCUS       CP133700             2490778 bp    DNA     circular BCT 05-SEP-2023
       HDRNA_20_K01_conservative_43457.current.gb:LOCUS       CP133701                2241 bp    DNA     circular BCT 05-SEP-2023
   
   ln -s /home/jhuang/Tools/spandx/ spandx
   
   nextflow run spandx/main.nf --fastq "trimmed_HDRNA_01/*_P_{1,2}.fastq.gz" --ref db/CP133676.fasta --annotation --database CP133676 -resume
   mv work work_CP133676
   mv Outputs Outputs_CP133676
   
   for fasta_file in CP133677 CP133678 CP133679 CP133680 CP133681 CP133682 CP133683 CP133684 CP133685 CP133686 CP133687 CP133688 CP133689 CP133690 CP133691 CP133692 CP133693 CP133694 CP133695 CP133696 CP133697 CP133698 CP133699 CP133700 CP133701; do
     echo "nextflow run spandx/main.nf --fastq "trimmed_HDRNA_01/*_P_{1,2}.fastq.gz" --ref db/${fasta_file}.fasta --annotation --database ${fasta_file} -resume"
     echo "mv work work_${fasta_file}"
     echo "mv Outputs Outputs_${fasta_file}"
   done
   
   for file in *.fastq.gz; do mv $file $(echo $file | cut -d'_' -f1)-$(echo $file | cut -d'_' -f1)-$(echo $file | cut -d'_' -f3)_$(echo $file | cut -d'_' -f6); done
   
   for file in *.fastq.gz; do mv $file $(echo $file | cut -d'_' -f3)_$(echo $file | cut -d'_' -f6); done
   for file in *.fastq.gz; do mv $file $(echo $file | cut -d'_' -f1)-$(echo $file | cut -d'_' -f2); done
   for file in *.fastq.gz; do mv $file $(echo $file | cut -d'-' -f1)_$(echo $file | cut -d'-' -f2); done
   
   Input read files could not be found.
   Have you included the read files in the current directory and do they have the correct naming?
   With the parameters specified, SPANDx is looking for reads named *_{1,2}.fastq.gz.
   To fix this error either rename your reads to match this formatting or specify the desired format
   when initializing SPANDx e.g. --fastq "*_{1,2}_sequence.fastq.gz"
   
   cd trimmed_HDRNA_01
   nextflow run ../spandx/main.nf --ref ../db/CP133676.fasta --annotation --database CP133676 -resume
   mv Outputs Outputs_CP133676
   cd ..
   
   cd trimmed_HDRNA_03
   nextflow run ../spandx/main.nf --ref ../db/CP133677.fasta --annotation --database CP133677 -resume
   mv Outputs Outputs_CP133677
   cd ..
   
   cd trimmed_HDRNA_06
   nextflow run ../spandx/main.nf --ref ../db/CP133678.fasta --annotation --database CP133678 -resume
   mv work work_CP133678
   mv Outputs Outputs_CP133678
   nextflow run ../spandx/main.nf --ref ../db/CP133679.fasta --annotation --database CP133679 -resume
   mv work work_CP133679
   mv Outputs Outputs_CP133679
   cd ..
   
   cd trimmed_HDRNA_07
   nextflow run ../spandx/main.nf --ref ../db/CP133680.fasta --annotation --database CP133680 -resume
   mv work work_CP133680
   mv Outputs Outputs_CP133680
   nextflow run ../spandx/main.nf --ref ../db/CP133681.fasta --annotation --database CP133681 -resume
   mv work work_CP133681
   mv Outputs Outputs_CP133681
   cd ..
   
   cd trimmed_HDRNA_08
   nextflow run ../spandx/main.nf --ref ../db/CP133682.fasta --annotation --database CP133682 -resume
   mv work work_CP133682
   mv Outputs Outputs_CP133682
   nextflow run ../spandx/main.nf --ref ../db/CP133683.fasta --annotation --database CP133683 -resume
   mv work work_CP133683
   mv Outputs Outputs_CP133683
   cd ..
   
   cd trimmed_HDRNA_12
   nextflow run ../spandx/main.nf --ref ../db/CP133684.fasta --annotation --database CP133684 -resume
   mv work work_CP133684
   mv Outputs Outputs_CP133684
   nextflow run ../spandx/main.nf --ref ../db/CP133685.fasta --annotation --database CP133685 -resume
   mv work work_CP133685
   mv Outputs Outputs_CP133685
   nextflow run ../spandx/main.nf --ref ../db/CP133686.fasta --annotation --database CP133686 -resume
   mv work work_CP133686
   mv Outputs Outputs_CP133686
   nextflow run ../spandx/main.nf --ref ../db/CP133687.fasta --annotation --database CP133687 -resume
   mv work work_CP133687
   mv Outputs Outputs_CP133687
   cd ..
   
   cd trimmed_HDRNA_16
   nextflow run ../spandx/main.nf --ref ../db/CP133688.fasta --annotation --database CP133688 -resume
   mv work work_CP133688
   mv Outputs Outputs_CP133688
   nextflow run ../spandx/main.nf --ref ../db/CP133689.fasta --annotation --database CP133689 -resume
   mv work work_CP133689
   mv Outputs Outputs_CP133689
   nextflow run ../spandx/main.nf --ref ../db/CP133690.fasta --annotation --database CP133690 -resume
   mv work work_CP133690
   mv Outputs Outputs_CP133690
   nextflow run ../spandx/main.nf --ref ../db/CP133691.fasta --annotation --database CP133691 -resume
   mv work work_CP133691
   mv Outputs Outputs_CP133691
   nextflow run ../spandx/main.nf --ref ../db/CP133692.fasta --annotation --database CP133692 -resume
   mv work work_CP133692
   mv Outputs Outputs_CP133692
   cd ..
   
   cd trimmed_HDRNA_17
   nextflow run ../spandx/main.nf --ref ../db/CP133693.fasta --annotation --database CP133693 -resume
   mv work work_CP133693
   mv Outputs Outputs_CP133693
   nextflow run ../spandx/main.nf --ref ../db/CP133694.fasta --annotation --database CP133694 -resume
   mv work work_CP133694
   mv Outputs Outputs_CP133694
   nextflow run ../spandx/main.nf --ref ../db/CP133695.fasta --annotation --database CP133695 -resume
   mv work work_CP133695
   mv Outputs Outputs_CP133695
   cd ..
   
   cd trimmed_HDRNA_19
   nextflow run ../spandx/main.nf --ref ../db/CP133696.fasta --annotation --database CP133696 -resume
   mv work work_CP133696
   mv Outputs Outputs_CP133696
   nextflow run ../spandx/main.nf --ref ../db/CP133697.fasta --annotation --database CP133697 -resume
   mv work work_CP133697
   mv Outputs Outputs_CP133697
   nextflow run ../spandx/main.nf --ref ../db/CP133698.fasta --annotation --database CP133698 -resume
   mv work work_CP133698
   mv Outputs Outputs_CP133698
   nextflow run ../spandx/main.nf --ref ../db/CP133699.fasta --annotation --database CP133699 -resume
   mv work work_CP133699
   mv Outputs Outputs_CP133699
   cd ..
   
   cd trimmed_HDRNA_20
   nextflow run ../spandx/main.nf --ref ../db/CP133700.fasta --annotation --database CP133700 -resume
   mv work work_CP133700
   mv Outputs Outputs_CP133700
   nextflow run ../spandx/main.nf --ref ../db/CP133701.fasta --annotation --database CP133701 -resume
   mv work work_CP133701
   mv Outputs Outputs_CP133701
   cd ..
   
   #-------------------------
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_01/Outputs_CP133676 .
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_03/Outputs_CP133677 .
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_06/Outputs_CP133678 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_06/Outputs_CP133679 .
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_07/Outputs_CP133680 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_07/Outputs_CP133681 .
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_08/Outputs_CP133682 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_08/Outputs_CP133683 .
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_12/Outputs_CP133684 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_12/Outputs_CP133685 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_12/Outputs_CP133686 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_12/Outputs_CP133687 .
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_16/Outputs_CP133688 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_16/Outputs_CP133689 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_16/Outputs_CP133690 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_16/Outputs_CP133691 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_16/Outputs_CP133692 .
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_17/Outputs_CP133693 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_17/Outputs_CP133694 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_17/Outputs_CP133695 .
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_19/Outputs_CP133696 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_19/Outputs_CP133697 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_19/Outputs_CP133698 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_19/Outputs_CP133699 .
   
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_20/Outputs_CP133700 .
   rsync -a -P jhuang@hamm:/home/jhuang/DATA/Data_Holger_S.epidermidis_short/trimmed_HDRNA_20/Outputs_CP133701 .
   
   cut -f2 -d$'\t' snippy.core.tab > f2
   cut -f3 -d$'\t' snippy.core.tab > f3
   cut -f4 -d$'\t' snippy.core.tab > f4
   
   diff snippy/merged_snp.vcf.id variants/f2
   5d5
   < 138824
   7d6
   < 139197
   9d7
   < 139844
   61d58
   < 2475573
   
   # -- merging vcf-files using bcftools --
   
   results_HDRNA_01/snippy
   bcftools merge HDRNA_01_K01/HDRNA_01_K01.vcf.gz HDRNA_01_K02/HDRNA_01_K02.vcf.gz HDRNA_01_K03/HDRNA_01_K03.vcf.gz HDRNA_01_K04/HDRNA_01_K04.vcf.gz HDRNA_01_K05/HDRNA_01_K05.vcf.gz HDRNA_01_K06/HDRNA_01_K06.vcf.gz HDRNA_01_K07/HDRNA_01_K07.vcf.gz HDRNA_01_K08/HDRNA_01_K08.vcf.gz HDRNA_01_K09/HDRNA_01_K09.vcf.gz HDRNA_01_K10/HDRNA_01_K10.vcf.gz -o merged.vcf
   #bcftools index merged.vcf.gz
   cp merged.vcf merged_CP133676.vcf
   
   cd results_HDRNA_03/snippy
   bcftools merge HDRNA_03_K01/HDRNA_03_K01.vcf.gz HDRNA_03_K02/HDRNA_03_K02.vcf.gz HDRNA_03_K03/HDRNA_03_K03.vcf.gz HDRNA_03_K04/HDRNA_03_K04.vcf.gz HDRNA_03_K05/HDRNA_03_K05.vcf.gz HDRNA_03_K06/HDRNA_03_K06.vcf.gz HDRNA_03_K07/HDRNA_03_K07.vcf.gz HDRNA_03_K08/HDRNA_03_K08.vcf.gz HDRNA_03_K09/HDRNA_03_K09.vcf.gz HDRNA_03_K10/HDRNA_03_K10.vcf.gz -o merged.vcf
   cp merged.vcf merged_CP133677.vcf
   
   cd results_HDRNA_06/snippy
   bcftools merge HDRNA_06_K01/HDRNA_06_K01.vcf.gz HDRNA_06_K02/HDRNA_06_K02.vcf.gz HDRNA_06_K03/HDRNA_06_K03.vcf.gz HDRNA_06_K04/HDRNA_06_K04.vcf.gz HDRNA_06_K05/HDRNA_06_K05.vcf.gz HDRNA_06_K06/HDRNA_06_K06.vcf.gz HDRNA_06_K07/HDRNA_06_K07.vcf.gz HDRNA_06_K08/HDRNA_06_K08.vcf.gz HDRNA_06_K09/HDRNA_06_K09.vcf.gz HDRNA_06_K10/HDRNA_06_K10.vcf.gz -o merged.vcf
   #split merged.vcf to merged_CP133678.vcf and merged_CP133679.vcf
   
   cd results_HDRNA_07/snippy
   bcftools merge HDRNA_07_K01/HDRNA_07_K01.vcf.gz HDRNA_07_K02/HDRNA_07_K02.vcf.gz HDRNA_07_K03/HDRNA_07_K03.vcf.gz HDRNA_07_K04/HDRNA_07_K04.vcf.gz HDRNA_07_K05/HDRNA_07_K05.vcf.gz HDRNA_07_K06/HDRNA_07_K06.vcf.gz HDRNA_07_K07/HDRNA_07_K07.vcf.gz HDRNA_07_K08/HDRNA_07_K08.vcf.gz HDRNA_07_K09/HDRNA_07_K09.vcf.gz HDRNA_07_K10/HDRNA_07_K10.vcf.gz -o merged.vcf
   cp merged.vcf merged_CP133680.vcf
   #Note that merged_CP133681.vcf is empty.
   
   cd results_HDRNA_08/snippy
   bcftools merge HDRNA_08_K01/HDRNA_08_K01.vcf.gz HDRNA_08_K02/HDRNA_08_K02.vcf.gz HDRNA_08_K03/HDRNA_08_K03.vcf.gz HDRNA_08_K04/HDRNA_08_K04.vcf.gz HDRNA_08_K05/HDRNA_08_K05.vcf.gz HDRNA_08_K06/HDRNA_08_K06.vcf.gz HDRNA_08_K07/HDRNA_08_K07.vcf.gz HDRNA_08_K08/HDRNA_08_K08.vcf.gz HDRNA_08_K09/HDRNA_08_K09.vcf.gz HDRNA_08_K10/HDRNA_08_K10.vcf.gz -o merged.vcf
   #split merged.vcf to merged_CP133682.vcf and merged_CP133683.vcf.
   #----ERROR: IGNORING the record---->
   #CP133683        1718    .       G       A       155736  .       QR=0;RO=0;ANN=A|intron_variant|MODIFIER|RGR12_11570|GENE_RGR12_11570|transcript|TRANSCRIPT_RGR12_11570|protein_coding|1/1|c.358-506C>T||||||WARNING_TRANSCRIPT_NO_START_CODON;DP=12890;AB=0;AO=3768;QA=121701;TYPE=snp  GT:DP:RO:QR:AO:QA:GL    ./.:.:.:.:.:.:. 1/1:5361:0:0:5347:173706:-15627.9,-1609.61,0    1/1:3750:0:0:3747:121191:-10903.3,-1127.96,0    ./.:.:.:.:.:.:. 1/1:3779:0:0:3768:121701:-10949.3,-1134.28,0    ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:. ./.:.:.:.:.:.:.
   
   cd results_HDRNA_12/snippy
   bcftools merge HDRNA_12_K01/HDRNA_12_K01.vcf.gz HDRNA_12_K02/HDRNA_12_K02.vcf.gz HDRNA_12_K03/HDRNA_12_K03.vcf.gz HDRNA_12_K04/HDRNA_12_K04.vcf.gz HDRNA_12_K05/HDRNA_12_K05.vcf.gz HDRNA_12_K06/HDRNA_12_K06.vcf.gz HDRNA_12_K07/HDRNA_12_K07.vcf.gz HDRNA_12_K08/HDRNA_12_K08.vcf.gz HDRNA_12_K09/HDRNA_12_K09.vcf.gz HDRNA_12_K10/HDRNA_12_K10.vcf.gz -o merged.vcf
   #split merged.vcf to merged_CP133684.vcf and merged_CP133685.vcf.
   #Note that merged_CP133686.vcf and merged_CP133687.vcf are empty.
   
   cd results_HDRNA_16/snippy
   bcftools merge HDRNA_16_K01/HDRNA_16_K01.vcf.gz HDRNA_16_K02/HDRNA_16_K02.vcf.gz HDRNA_16_K03/HDRNA_16_K03.vcf.gz HDRNA_16_K04/HDRNA_16_K04.vcf.gz HDRNA_16_K05/HDRNA_16_K05.vcf.gz HDRNA_16_K06/HDRNA_16_K06.vcf.gz HDRNA_16_K07/HDRNA_16_K07.vcf.gz HDRNA_16_K08/HDRNA_16_K08.vcf.gz HDRNA_16_K09/HDRNA_16_K09.vcf.gz HDRNA_16_K10/HDRNA_16_K10.vcf.gz -o merged.vcf
   cp merged.vcf merged_CP133688.vcf
   #Note that merged_CP133689.vcf - merged_CP133692.vcf are empty.
   
   cd results_HDRNA_17/snippy
   bcftools merge HDRNA_17_K01/HDRNA_17_K01.vcf.gz HDRNA_17_K02/HDRNA_17_K02.vcf.gz HDRNA_17_K03/HDRNA_17_K03.vcf.gz HDRNA_17_K04/HDRNA_17_K04.vcf.gz HDRNA_17_K05/HDRNA_17_K05.vcf.gz HDRNA_17_K06/HDRNA_17_K06.vcf.gz HDRNA_17_K07/HDRNA_17_K07.vcf.gz HDRNA_17_K08/HDRNA_17_K08.vcf.gz HDRNA_17_K09/HDRNA_17_K09.vcf.gz HDRNA_17_K10/HDRNA_17_K10.vcf.gz -o merged.vcf
   cp merged.vcf merged_CP133693.vcf
   #Note that merged_CP133694.vcf - merged_CP133695.vcf are empty.
   
   cd results_HDRNA_19/snippy
   bcftools merge HDRNA_19_K01/HDRNA_19_K01.vcf.gz HDRNA_19_K02/HDRNA_19_K02.vcf.gz HDRNA_19_K03/HDRNA_19_K03.vcf.gz HDRNA_19_K04/HDRNA_19_K04.vcf.gz HDRNA_19_K05/HDRNA_19_K05.vcf.gz HDRNA_19_K06/HDRNA_19_K06.vcf.gz HDRNA_19_K07/HDRNA_19_K07.vcf.gz HDRNA_19_K08/HDRNA_19_K08.vcf.gz HDRNA_19_K09/HDRNA_19_K09.vcf.gz HDRNA_19_K10/HDRNA_19_K10.vcf.gz -o merged.vcf
   cp merged.vcf merged_CP133696.vcf
   #Note that merged_CP133697.vcf - merged_CP133699.vcf are empty.
   
   cd results_HDRNA_20/snippy
   bcftools merge HDRNA_20_K01/HDRNA_20_K01.vcf.gz HDRNA_20_K02/HDRNA_20_K02.vcf.gz HDRNA_20_K03/HDRNA_20_K03.vcf.gz HDRNA_20_K04/HDRNA_20_K04.vcf.gz HDRNA_20_K05/HDRNA_20_K05.vcf.gz HDRNA_20_K06/HDRNA_20_K06.vcf.gz HDRNA_20_K07/HDRNA_20_K07.vcf.gz HDRNA_20_K08/HDRNA_20_K08.vcf.gz HDRNA_20_K09/HDRNA_20_K09.vcf.gz -o merged.vcf
   cp merged.vcf merged_CP133700.vcf
   #Note that merged_CP133701.vcf is empty.
   #Note not enough reads exist in 'HDRNA_20 S K10 365_BB84_S87_R1_001.fastq.gz' and 'HDRNA_20 S K10 365_BB84_S87_R2_001.fastq.gz'.
   
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_01/snippy/merged_CP133676.vcf Outputs_CP133676/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_01_not_in_vcf_file_output.txt HDRNA_01_not_in_txt_file_output.txt HDRNA_01_common_records_output.txt
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_03/snippy/merged_CP133677.vcf Outputs_CP133677/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_03_not_in_vcf_file_output.txt HDRNA_03_not_in_txt_file_output.txt HDRNA_03_common_records_output.txt
   
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_06/snippy/merged_CP133678.vcf Outputs_CP133678/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_06_1_not_in_vcf_file_output.txt HDRNA_06_1_not_in_txt_file_output.txt HDRNA_06_1_common_records_output.txt
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_06/snippy/merged_CP133679.vcf Outputs_CP133679/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_06_2_not_in_vcf_file_output.txt HDRNA_06_2_not_in_txt_file_output.txt HDRNA_06_2_common_records_output.txt
   
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_07/snippy/merged_CP133680.vcf Outputs_CP133680/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_07_not_in_vcf_file_output.txt HDRNA_07_not_in_txt_file_output.txt HDRNA_07_common_records_output.txt
   
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_08/snippy/merged_CP133682.vcf Outputs_CP133682/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_08_not_in_vcf_file_output.txt HDRNA_08_not_in_txt_file_output.txt HDRNA_08_common_records_output.txt
   #ERROR: python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_08/snippy/merged_CP133683.vcf Outputs_CP133683/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_08_2_not_in_vcf_file_output.txt HDRNA_08_2_not_in_txt_file_output.txt HDRNA_08_2_common_records_output.txt
   
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_12/snippy/merged_CP133684.vcf Outputs_CP133684/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_12_1_not_in_vcf_file_output.txt HDRNA_12_1_not_in_txt_file_output.txt HDRNA_12_1_common_records_output.txt
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_12/snippy/merged_CP133685.vcf Outputs_CP133685/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_12_2_not_in_vcf_file_output.txt HDRNA_12_2_not_in_txt_file_output.txt HDRNA_12_2_common_records_output.txt
   
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_16/snippy/merged_CP133688.vcf Outputs_CP133688/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_16_not_in_vcf_file_output.txt HDRNA_16_not_in_txt_file_output.txt HDRNA_16_common_records_output.txt
   
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_17/snippy/merged_CP133693.vcf Outputs_CP133693/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_17_not_in_vcf_file_output.txt HDRNA_17_not_in_txt_file_output.txt HDRNA_17_common_records_output.txt
   
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_19/snippy/merged_CP133696.vcf Outputs_CP133696/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_19_not_in_vcf_file_output.txt HDRNA_19_not_in_txt_file_output.txt HDRNA_19_common_records_output.txt
   
   python3 ~/Scripts/merge_snippy_and_spandx_results.py results_HDRNA_20/snippy/merged_CP133700.vcf Outputs_CP133700/Phylogeny_and_annotation/All_SNPs_indels_annotated.txt HDRNA_20_not_in_vcf_file_output.txt HDRNA_20_not_in_txt_file_output.txt HDRNA_20_common_records_output.txt
   
   mv HDRNA_01_common_records_output.txt _HDRNA_01.txt
   mv HDRNA_03_common_records_output.txt  HDRNA_03.txt
   mv HDRNA_06_common_records_output.txt  HDRNA_06.txt
   mv HDRNA_07_common_records_output.txt  HDRNA_07.txt
   mv HDRNA_08_common_records_output.txt  HDRNA_08.txt
   mv HDRNA_12_common_records_output.txt  HDRNA_12.txt
   mv HDRNA_16_common_records_output.txt  HDRNA_16.txt
   mv HDRNA_17_common_records_output.txt  HDRNA_17.txt
   mv HDRNA_19_common_records_output.txt  HDRNA_19.txt
   mv HDRNA_20_common_records_output.txt  HDRNA_20.txt
   
   sed -i '1s/_trimmed_P//g' _HDRNA_01.txt
   sed -i '1s/_trimmed_P//g' HDRNA_03.txt HDRNA_06.txt HDRNA_07.txt HDRNA_08.txt HDRNA_12.txt HDRNA_16.txt HDRNA_17.txt HDRNA_19.txt HDRNA_20.txt
   
   # -- check if f3==f6 --
   cut -f3 -d$'\t' HDRNA_17.txt > f3
   cut -f6 -d$'\t' HDRNA_17.txt > f6
   diff f3 f6
   
   # -- check if f6==f7 in HDRNA_7.txt since they have the sample names --
   cut HDRNA_07.txt -d$'\t' -f6  > f6
   cut HDRNA_07.txt -d$'\t' -f7  > f7
   diff d6 f7
   --> delete the column HDRNA_07_K01-BB28 in variant_calling.xls.
   
   ~/Tools/csv2xls-0.4/csv_to_xls.py _HDRNA_01.txt HDRNA_03.txt HDRNA_06.txt HDRNA_07.txt HDRNA_08.txt HDRNA_12.txt HDRNA_16.txt HDRNA_17.txt HDRNA_19.txt HDRNA_20.txt -d$'\t' -o variant_calling.xls
   

5. processing commands for presence phage HH1, SPbeta-like phage, phage related island

   #makeblastdb -in HDRNA_K01.fna -dbtype nucl
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_01.blastn
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_01.blastn
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_01.blastn
   
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_03.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_03.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_03.blastn
   
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_06.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_06.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_06.blastn
   
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_07.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_07.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_07.blastn
   
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_08.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_08.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_08.blastn
   
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_12.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_12.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_12.blastn
   
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_16.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_16.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_16.blastn
   
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_17.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_17.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_17.blastn
   
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_19.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_19.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_19.blastn
   
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query MT880870.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880870_on_20.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query MT880871.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880871_on_20.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query MT880872.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > MT880872_on_20.blastn
   
   ΦSepi-HH1(MT880870): 34053 bp in ST2, ST83 (34053 bt)
   PI-Sepi-HH2(MT880871): not in ST2, but in ST290, ST297 and ST487 (36164 bt)
   ΦSPbeta-like(MT880872): in ST2 and ST22 (147057 bt)
   # In the new isolates, we have the MLST
   
   -
   ST130
   ST224
   ST23
   ST35
   ST487 -->
   ST5
   ST640
   ST69
   ST86
   ST87
   --> HDRNA_17_K01 (ST69) contains MT880871!
   It agrees with the description in the Anna's paper, ST487 has PI-Sepi-HH2!
   #shovill/HDRNA_11_K01/contigs.fa sepidermidis    487     arcC(1) aroE(1) gtr(1)  mutS(5) pyrR(2) tpiA(1) yqiL(1)
   
   # -- 01 --
   33342   34053 --> am Grenzen
   33634   34132 --> am Grenzen
   131829  147057 + 1       3810 --> am Grenzen
   30857   34053 --> NA
   33634   34132 --> NA
   131829  147057 + 1       3807 --> NA
   NA
   NA
   NA
   07: NA
   08: NA
   12: NA
   16: NA
   17: MT880871_on_17.blastn YES
   19: NA
   20: NA
   
   shovill/HDRNA_11_K01/contigs.fa sepidermidis    487     arcC(1) aroE(1) gtr(1)  mutS(5) pyrR(2) tpiA(1) yqiL(1)
   
   a Biofilm
   formation compared to S. epidermidis 1457: –, ⬍30%; ⫹, 30% to 59%; ⫹⫹, 60% to 84%; ⫹⫹⫹, ⱖ85%.
   b ST,
   sequence type determined by MLST.
   c GC, genetic cluster based on Bayesian analysis of population structure (BAPS) of MLST.
   d ND, not determined. In columns 2 to 5, ⫹ indicates presence and ⫺ indicates absence.
   
   ND, not determined or defined. '+' indicates presence and '-' indicates absence.
   
   SPbeta-like staphylococcus phage (NC_029119.1, 86% sequence identity)[47] and will here be referred to as
   ΦSPbeta-like, (GenBank accession number MT880872) the remaining two regions did not correspond to any previously described Staphylococcus phage[48]
   ΦSepi-HH1 (MT880870): 34053 bp
   phage-related island PI-Sepi-HH2 (MT880871).
   MT880870.1: Staphylococcus phage PhiSepi-HH1, complete genome
   MT880871.1: Staphylococcus phage PI-Sepi-HH2, complete genome: 36164 bp
   MT880872.1: Staphylococcus phage PhiSepi-HH3, complete genome
   

6. processing commands for the other genes from Gene_List.pptx

           # AND "Staphylococcus epidermidis"[porgn:__txid1282]
   
   mv HDRNA_16_K01_conservative_37834.current.gb ../gbk
   mv ./HDRNA_17_K01_conservative_37288.current.gb ../gbk
   mv ./HDRNA_03_K01_bold_bandage_26831.current.gb ../gbk
   mv ./HDRNA_06_K01_conservative_27645.current.gb ../gbk
   mv ./HDRNA_12_K01_bold_37467.current.gb ../gbk
   mv ./HDRNA_01_K01_conservative_23197.current.gb ../gbk
   mv ./HDRNA_07_K01_conservative_27169.current.gb ../gbk
   mv ./HDRNA_08_K01_conservative_32455.current.gb ../gbk
   mv ./HDRNA_19_K01_bold_37377.current.gb ../gbk
   mv ./HDRNA_20_K01_conservative_43457.current.gb ../gbk
   
   (agrC) AND "Staphylococcus"
   https://www.ncbi.nlm.nih.gov/nuccore/OQ828637.1
   
   gltA
   agrC
   
   gene            2184799..2186091
                       /gene="agrC"
                       /locus_tag="SAR2125"
       CDS             2184799..2186091
                       /gene="agrC"
                       /locus_tag="SAR2125"
                       /note="Signal dectecting component of the agr autoinducer
                       peptide-quorum sensing system. Two-component regulatory
                       system family, sensor kinase protein. Similar to
                       Staphylococcus aureus accessory gene regulator C AgrC
                       TR:Q53644 (EMBL:X52543) (423 aa) fasta scores: E():
                       1.7e-101, 75.23% id in 424 aa, and to Staphylococcus
                       epidermidis histidine kinase AgrC TR:O68159
                       (EMBL:AF012132) (429 aa) fasta scores: E(): 6.3e-76,
                       54.93% id in 426 aa"
                       /codon_start=1
                       /transl_table=11
                       /product="autoinducer sensor protein"
                       /protein_id="CAG41106.1"
                       /db_xref="EnsemblGenomes-Gn:SAR2125"
                       /db_xref="EnsemblGenomes-Tr:CAG41106"
                       /translation="MEALNDYNYVLFVIVQVSLMFFISAFISGIRYKKSDYIYIIGIV
                       LSSVYFFDKIRSISLVVITIFIIIFLYFKIRLYSVFLVMVTQIILYCANFVYIIIFSY
                       IITISHSVFIVLPIFLVVYVSISYALAYILNRILKRINGTYLSLNKKFLTVITIVIVI
                       TFSLLFAYSQIDASDASTIKQYSLLFLGIIILLSILIFIYSQFTLKEMKYKRNQEEIE
                       TYYEYTLKIEAINNEMRKFRHDYVNILTTLSEYIREDDMTGLRDYFNKNIVPMKDNLQ
                       MNALKLNGIENLKVREIKGLLTAKILRAQEMNIPISIEIPDEVTRINLNMIDLSRSIG
                       IILDNAIEASSEIDDPIIRVAFIESENSVTFIVMNKCADDIPRIHELFQESFSTKGEG
                       RGLGLSTLKEIADNADNVLLDTIIENGFFIQKVEIINN"
   MEALNDYNYVLFVIVQVSLMFFISAFISGIRYKKSDYIYIIGIVLSSVYFFDKIRSISLVVITIFIIIFLYFKIRLYSVFLVMVTQIILYCANFVYIIIFSYIITISHSVFIVLPIFLVVYVSISYALAYILNRILKRINGTYLSLNKKFLTVITIVIVITFSLLFAYSQIDASDASTIKQYSLLFLGIIILLSILIFIYSQFTLKEMKYKRNQEEIETYYEYTLKIEAINNEMRKFRHDYVNILTTLSEYIREDDMTGLRDYFNKNIVPMKDNLQMNALKLNGIENLKVREIKGLLTAKILRAQEMNIPISIEIPDEVTRINLNMIDLSRSIGIILDNAIEASSEIDDPIIRVAFIESENSVTFIVMNKCADDIPRIHELFQESFSTKGEGRGLGLSTLKEIADNADNVLLDTIIENGFFIQKVEIINN
   Staphylococcus_aureus_MRSA252
   
   samtools faidx Staphylococcus_aureus_MRSA252.fasta "gi|49240382|emb|BX571856.1|":2184799-2186091
   
   (yycG) AND "Staphylococcus"
       gene            25617..27443
                       /gene="yycG"
                       /locus_tag="SAR0019"
                       /gene_synonym="vicK"
       CDS             25617..27443
                       /gene="yycG"
                       /locus_tag="SAR0019"
                       /gene_synonym="vicK"
                       /note="Two-component regulatory system family, sensor
                       kinase protein. Previously sequenced as Staphylococcus
                       aureus two-component sensor histidine kinase YycG
                       TR:Q9XCM6 (EMBL:AF136709) (608 aa) fasta scores: E():
                       5.5e-214, 99.836% id in 608 aa. Similar to Bacillus
                       subtilis probable two-component sensor histidine kinase
                       YycG TR:Q45614 (EMBL:D78193) (611 aa) fasta scores: E():
                       2e-98, 46.217% id in 608 aa"
                       /codon_start=1
                       /transl_table=11
                       /product="sensor kinase protein"
                       /protein_id="CAG39047.1"
                       /db_xref="EnsemblGenomes-Gn:SAR0019"
                       /db_xref="EnsemblGenomes-Tr:CAG39047"
                       /db_xref="GOA:Q6GKS6"
                       /db_xref="InterPro:IPR000014"
                       /db_xref="InterPro:IPR000700"
                       /db_xref="InterPro:IPR003594"
                       /db_xref="InterPro:IPR003660"
                       /db_xref="InterPro:IPR003661"
                       /db_xref="InterPro:IPR004358"
                       /db_xref="InterPro:IPR005467"
                       /db_xref="InterPro:IPR029151"
                       /db_xref="UniProtKB/Swiss-Prot:Q6GKS6"
                       /translation="MKWLKQLQSLHTKLVIVYVLLIIIGMQIIGLYFTNNLEKELLDN
                       FKKNITQYAKQLEISIEKVYDEKGSVNAQKDIQNLLSEYANRQEIGEIRFIDKDQIII
                       ATTKQSNRSLINQKANDSSVQKALSLGQSNDHLILKDYGGGKDRVWVYNIPVKVDKKV
                       IGNIYIESKINDVYNQLNNINQIFIVGTAISLLITVILGFFIARTITKPITDMRNQTV
                       EMSRGNYTQRVKIYGNDEIGELALAFNNLSKRVQEAQANTESEKRRLDSVITHMSDGI
                       IATDRRGRIRIVNDMALKMLGMAKEDIIGYYMLSVLSLEDEFKLEEIQENNDSFLLDL
                       NEEEGLIARVNFSTIVQETGFVTGYIAVLHDVTEQQQVERERREFVANVSHELRTPLT
                       SMNSYIEALEEGAWKDEELAPQFLSVTREETERMIRLVNDLLQLSKMDNESDQINKEI
                       IDFNMFINKIINRHEMSTKDTTFIRDIPKKTIFTEFDPDKMTQVFDNVITNAMKYSRG
                       DKRVEFHVKQNPLYNRMTIRIKDNGIGIPINKVDKIFDRFYRVDKARTRKMGGTGLGL
                       AISKEIVEAHNGRIWANSVEGQGTSIFITLPCEVIEDGDWDE"
   
   samtools faidx Staphylococcus_aureus_MRSA252.fasta "gi|49240382|emb|BX571856.1|":25617-27443
   
   psmß1: https://www.ncbi.nlm.nih.gov/nuccore/380448412
   hlb: https://www.ncbi.nlm.nih.gov/nuccore/KC242859.1
   
   atlE
   
   tagB
   
       gene            694999..696102
                       /gene="tagB"
                       /locus_tag="SAR0649"
       CDS             694999..696102
                       /gene="tagB"
                       /locus_tag="SAR0649"
                       /note="Similar to Bacillus subtilis teichoic acid
                       biosynthesis protein B TagB SW:TAGB_BACSU (P27621) (381
                       aa) fasta scores: E(): 4.3e-26, 31.302% id in 361 aa, and
                       to Lactococcus lactis teichoic acid biosynthesis protein B
                       TagB TR:Q9CH14 (EMBL:AE006327) (371 aa) fasta scores: E():
                       2.8e-06, 24.834% id in 302 aa. Lack of similarity at the
                       N-terminus in comparison to other orthologues"
                       /codon_start=1
                       /transl_table=11
                       /product="teichoic acid biosynthesis protein"
                       /protein_id="CAG39666.1"
                       /db_xref="EnsemblGenomes-Gn:SAR0649"
                       /db_xref="EnsemblGenomes-Tr:CAG39666"
                       /translation="MNVLIKKFYHLVVRILSKMITPQVIDKPHIVFMMTFPEDIKPII
                       KALNNSLYQKTVLTTPKQAPYLSELSDDVNVIEMTNRTLVKQIKALKSAQMIIIDNYY
                       LLLGGYNKTSNQHIVQTWHASGALKNFGLTDHQVDVSDKAMVQQYRKVYQATDFYLVG
                       CEQMSQCFKQSLGATEEQMLYFGLPRINKYYTADRATVKAELKDKYGITNKLALYVPT
                       YREDKADNRAIDKAYFEKCLPGYTLINKLHPSIEHSDIDDVSSIDTSILMLMSDIIIS
                       DYSSLPIEASLLDIPTIFYVYDEGTYDKVRGLNQFYKAIPDSYKVYTEEDLIMTIQEK
                       EHLLSPLFKDWHKYNTDKSLHQLTEYIDKMVTK"
   
   samtools faidx Staphylococcus_aureus_MRSA252.fasta "gi|49240382|emb|BX571856.1|":694999-696102 > tagB.fasta
   
       gene            2137..2586
                       /gene="capC"
       CDS             2137..2586
                       /gene="capC"
                       /codon_start=1
                       /transl_table=11
                       /product="CapC"
                       /protein_id="BAB13485.1"
                       /translation="MFGSDLYIALILGVLLSLIFAEKTGIVPAGLVVPGYLGLVFNQP
                       VFILLVLLVSLLTYVIVKYGLSKFMILYGRRKFAAMLITGIVLKIAFDFLYPIVPFEI
                       AEFRGIGIIVPGLIANTIQKQGLTITFGSTLLLSGATFAIMFVYYLI"
   
   samtools faidx capBCA_ywtC.fasta "gi|10119860|dbj|AB039950.1|":2137-2586 > capC.fasta
   
       gene            2783..3256
                       /gene="sepA"
       CDS             2783..3256
                       /gene="sepA"
                       /function="multidrug resistance"
                       /experiment="experimental evidence, no additional details
                       recorded"
                       /note="similar to BAB43260.1 of S. aureus N315"
                       /codon_start=1
                       /transl_table=11
                       /product="SepA"
                       /protein_id="BAB83937.1"
                       /translation="MIVNYLKHKFYNLLTTMIVLFIFVLSGAIFLTFLGFGLYGLSRI
                       LIYFRLGDFTYNRSMYDNLLYYGSYIIFGYFIIFAVEHLMDYFRKMLPENAYFRGATF
                       HLISYTVATTLFYFIIHLNYVYINIDFWVIMVIIGFLYVCKLQFYPESKNLNNRK"
   
   samtools faidx ORF123_sepA_ORF5.fasta "gi|18250967|dbj|AB078343.1|":2783-3256 > sepA.fasta
   
       gene            1427047..1429569
                       /gene="mprF"
                       /locus_tag="SAR1372"
                       /gene_synonym="fmtC"
       CDS             1427047..1429569
                       /gene="mprF"
                       /locus_tag="SAR1372"
                       /gene_synonym="fmtC"
                       /note="Similar to Staphylococcus aureus putative membrane
                       protein MprF TR:AAK58115 (EMBL:AF145699) (840 aa) fasta
                       scores: E(): 0, 96.190% id in 840 aa. Similar to
                       Staphylococcus xylosus putative membrane protein MprF
                       TR:AAK58113 (EMBL:AF145698) (841 aa) fasta scores: E():
                       5.4e-208, 62.530% id in 838 aa. Mutations in the CDS have
                       reduced resistance to human defensins and evasion of
                       neutrophil killing"
                       /codon_start=1
                       /transl_table=11
                       /product="putative membrane protein"
                       /protein_id="CAG40370.1"
                       /db_xref="EnsemblGenomes-Gn:SAR1372"
                       /db_xref="EnsemblGenomes-Tr:CAG40370"
                       /db_xref="GOA:Q6GH45"
                       /db_xref="InterPro:IPR016181"
                       /db_xref="InterPro:IPR022791"
                       /db_xref="InterPro:IPR024320"
                       /db_xref="UniProtKB/Swiss-Prot:Q6GH45"
                       /translation="MNQEVKNKIFSILKITFATALFIFVVITLYRELSGINFKDTLVE
                       FSKINRMSLVLLFIGGGASLVILSMYDVILSRALKMDISLGKVLRVSYIINALNAIVG
                       FGGFIGAGVRAMVYKNYTHDKKKLVHFISLILISMLTGLSLLSLLIVFHVFDASLILN
                       KITWVRWVLYAVSLFLPLFIIYSMVRPPDKNNRYVGLYCTLVSCVEWLAAAVVLYFCG
                       VIVDVHVSFMSFIAIFIIAALSGLVSFIPGGFGAFDLVVLLGFKTLGVPEEKVLLMLL
                       LYRFAYYFVPVIIALILSSFEFGTSAKKYIEGSKYFIPAKDVTSFLMSYQKDIIAKIP
                       SLSLAILVFFTSMIFFVNNLTIVYDALYDGNHLTYYLLLAIHTSACLLLLLNVVGIYK
                       QSRRAIIYAMISIILIIVATLFTYASYILITWLVIIFALLIVAFRRARRLKRPIRMRN
                       LVAMLLFSIFILYINHIFIAGTFYALDVYTIEMHTSVLKYYFWITILIIAIIVGAIAW
                       LFDYQFSKVRISSNIEECEEIIDQYGGNYLSHLIYSGDKQFFTNEDKNAFLMYRYKAS
                       SLVVLGDPIGDENAFDELLEAFYNYAEYLGYDVIFYQVTDQHMPLYHNFGNQFFKLGE
                       EAIIDLTQFSTSGKKRRGFRATLNKFDELNISFEIIEPPFSTEFINELQHVSDLWLDN
                       RQEMHFSVGQFNETYLSKAPIGVMRNENNEVIAFCSLMPTYFNDAISVDLIRWLPELD
                       LPLMDGLYLHMLLWSKEQGYTKFNMGMATLSNVGQLHYSYLRERLAGRVFEHFNGLYR
                       FQGLRRYKSKYNPNWEPRFLVYRKDNSLWESLSKVMRVIRHK"
   
   samtools faidx Staphylococcus_aureus_MRSA252.fasta "gi|49240382|emb|BX571856.1|":1427047-1429569 > fmtC.fasta
   
       gene            1825..2523
                       /gene="sceD"
       CDS             1825..2523
                       /gene="sceD"
                       /codon_start=1
                       /transl_table=11
                       /product="SceD precursor"
                       /protein_id="AAB94657.1"
                       /translation="MKKLLVASSASAALFAVGVGANAHAAEDNNVNQDQLAQTALNNT
                       QQLNDAPVQEGAYNIAFDNSGYNFNFNSDGTNWSWSYNADSSAQQAPAQSTTQEQAPA
                       AQQAPAQSTTQEQAPAAQQAPAQEQTQQPAQQPAQQQTQQPAQQSADSGSNVQVNDHL
                       KAIAQRESGGDIHAINSSSGAAGKYQFLQTTWDSVAPAEYQGKPASEAPEAVQDAAAQ
                       KLYDTAGPSQWVTA"
       sig_peptide     1825..1899
                       /gene="sceD"
       mat_peptide     1900..2520
                       /gene="sceD"
                       /product="SceD"
   
   samtools faidx sceDAE.fasta "gi|6707000|gb|AF109218.1|":1825-2523 > sceD.fasta
   
       gene            759097..759894
                       /locus_tag="SERP_RS03845"
                       /old_locus_tag="SE0760"
                       /old_locus_tag="SERP0760"
       CDS             759097..759894
                       /locus_tag="SERP_RS03845"
                       /old_locus_tag="SE0760"
                       /old_locus_tag="SERP0760"
                       /inference="COORDINATES: similar to AA
                       sequence:RefSeq:WP_001830106.1"
                       /note="Derived by automated computational analysis using
                       gene prediction method: Protein Homology."
                       /codon_start=1
                       /transl_table=11
                       /product="VOC family protein"
                       /protein_id="WP_002446237.1"
                       /db_xref="GI:488376852"
                       /translation="MFHNKNANFVNGVTINIKDKETIKTFYENVLGFNLINESKTAVQ
                       FEVGDSNQFITFIEIQNGREPLMSEAGLFHIGILLPTLTTLADLLVHLSDFEVPVNGG
                       QQSVATCLFIEDPEGNAIKFYVDRETESWIDEKEGRIRMDIAPINVPRLLQNVSHTQW
                       QGIPDETKLGSLHIKSIRISDVKSYYLHYFGLEESAYMDDYSLFLSSNDYYNHLAVNQ
                       WLSATKRVDNEHTYGLAMIDFHYPKTTHKNLKGPDGIYFRFNRIKEV"
   
   samtools faidx Staphylococcus_epidermidis_RP62A.fasta "gi|57865352|ref|NC_002976.3|":759097-759894 > SE0760.fasta
   
       gene            3091..8793
                       /gene="esp"
                       /allele="1"
       CDS             3091..8793
                       /gene="esp"
                       /allele="1"
                       /note="enterococcal surface protein; ORF3"
                       /codon_start=1
                       /transl_table=11
                       /product="Esp"
                       /protein_id="AAQ84025.1"
                       /translation="MVSKNNKRVFLEKTKKRVLKYSIKKLSVGVASVLVGVGLVLGTT
                       ELVQAQDEISPSTPLETAISSVQVGDKVASGNTFQENPGYTKNYNFSDLQFSPQELTG
                       DTLKGNTIGFEVYGKHNIAASTKNWEIRLQLDERLAKYVEKIQVDPKKGIGSSRRTFV
                       RINDSLGRPTNIWKVNYIRASDGLFAGAETTDTQTAPNGVITFEKSLDEIFKEIGIDN
                       LKTDRLMYRIYLVSHQDDDKIVPGIDSTGYFLTDSDDFYNSLDVSENNPDQFKHGSVS
                       AKYEEPNTQTKDGSGSTGANGAIILDHKLTKNYNFSYSASAKGTPWYANYKIDERLVP
                       YVAGIQMHMVQADKVTYDVSFESGKKVADLAIERRKDHENYGVGSITDNDLTKLIDFA
                       NASPRPVVIRYVLQLTKPLDEILEDMKATAQVEENKPFGEDFIFDSWLSDTNKKLIQN
                       TYGTGYYYLQDIDGDGNPDDKEESGDTNPYIGKPELEEVYDVDTTVKGKVFIHELAGT
                       GHKAQLVDKEGTVLAEKTIAPNEKDGAPISDTVEFEFTGVDSSKLIAKDELKIQIVSP
                       GFDKPEEGSTVIKESPKAVDKQTVVVGFKPDAKESIRNNKNLPEDAEYSWKTEPDTSN
                       VTDSTKGIVTVKIGNRTFDVDVEFAVKASQAMENDATYVPITTTPETTVQSGKPTFDK
                       PDVPLAKDAFSILDVYNKDFGNASVDANTGIVTFTPAKGVGESEPITGTIPIKIVYQD
                       GSVGTTDLAVTVSKDIYENPGENIPAGYHKVTFTAGEGTSIESGTTVFAVKDGVSLPE
                       DKLPVLKAKDGYTDAKWPEEATQPITADDTEFVSSATKLDDIIENPGENIPAGYHKVT
                       FTAGEGTSIESGTTVFAVKDGVSLPEDKLPVLKAKDGYTDAKWPEEATQPITADDTEF
                       VSSATKLDDIIENPGENIPAGYHKVTFTAGEGTSIESGTTVFAVKDGVSLPEDKLPVL
                       KAKDGYTDAKWPEEATQPITADDTEFVSSATKLDDIIENPGENIPAGYHKVIFTAGEG
                       TSIESGTTVFAVKDGVSLPEDKLPVLKAKDGYTDAKWPEEATQPITADDTEFVSSATK
                       LDDIIENPGENIPAGYHKVIFTAGEGTSIESGTTVFAVKDGVSLPEDKLPVLKAKDGY
                       TDAKWPEEATQPITADDTEFVSSATKLDDKSDADKYNPEGQKVTTELNKEPDASEGIK
                       NKEDLPKDTKYTWKEKVDVSAAGNKKGTVVVTYSDGSSDEVEVDVTVTDNRSDADKYE
                       PTVEGEKVEVGGTVDLTDNVTNLPTLPEGTTVTDVTPDGTIDTNTPGNYEGVIEVTYP
                       DGTKDTVKVPVEVTDNRSDADKYTPMVEGEKVEVGGTVDLTDNVTNLPTLPEGTTVTD
                       VTPDGTIDTNTPGNYEGVIEVTYPDGTKDTVKVPVEVTDNRSDADKYTPMVEGEKVEV
                       GGTVDLTDNVTNLPTLPEGTTVTDVTPGGTIDTNTPGNYEGVIEVTYPDGTKDTVKVP
                       VEVTDNRSDADKYEPTVEGEKVEVGGTVDLTDNVTNLPTLPEGTTVTDVTPGGTIDTN
                       TPGNYEGVIEVTYPDGTKDTVKVPVEVTDNRSDADKYTPMVEGEKVEVGGTVDLTDNV
                       TNLPTLPEGTTVTDVTPDGTIDTNTPGNYEGVIEVTYPDGTKDTVKVPVEVTDNRSDA
                       DKYNPEGQKVTTDLNKEPDASEGIKNKEDLPKGTTYTWKEKVDVSTAGNKKGIVVVTY
                       PDGSKEEVEVTISVEDKKAPNKPQVDPITEGDQIVTGKTEPNAEVTVTLPNGSQYHGT
                       ADKNGNFTVKVPKLEAGTKVIVTATDESGNTSEPTNVVVSSNEKDSEKAVSKDNKTDN
                       QGSKQNTNRGKSSPQKQSSKAYPKTGEIDSNIFTISGGLILLGTLGLLGYKNRKKENE
                       "
   samtools faidx Enterococcus_faecium_isolate_E300_pathogenicity_island.fasta "gi|34980227|gb|AY322150.1|":3091-8793 > esp.fasta
   
   mv ~/Downloads/sequence\ \(1\).fasta ecpA.fasta
   
   mv ~/Downloads/sequence\ \(1\).fasta sdrG.fasta
   
   HH1-HP1
   HH1-HP2
   HH1-TreR
   
   sdrG.fasta
   
   gltA.fasta
   agrC.fasta
   yycG.fasta
   atlE.fasta
   psm-beta1.fasta
       gene            366..500
                       /gene="psm beta1"
       CDS             366..500
                       /gene="psm beta1"
                       /note="hemolytic protein; pfam05480"
                       /codon_start=1
                       /transl_table=11
                       /product="Psm beta1"
                       /protein_id="AFD54319.1"
                       /translation="MEGLFNAIKDTVTAAINNDGAKLGTSIVSIVENGVGLLGKLFGF
                       "
       gene            557..691
                       /gene="psm beta2"
       CDS             557..691
                       /gene="psm beta2"
                       /note="hemolytic protein; pfam05480"
                       /codon_start=1
                       /transl_table=11
                       /product="Psm beta2"
                       /protein_id="AFD54320.1"
                       /translation="MTGLAEAIANTVQAAQQHDSVKLGTSIVDIVANGVGLLGKLFGF
                       "
   samtools faidx psm-beta.fasta "gi|380448412|gb|JQ066320.1|":366-500 > psm-beta1.fasta
   
   hlb.fasta
   samtools faidx hlb_.fasta "gi|441494790|gb|KC242859.1|":16-1008 > hlb.fasta
   tagB.fasta
   capC.fasta
   sepA.fasta
   fmtC.fasta
   sceD.fasta
   SE0760.fasta
   esp.fasta
   samtools faidx ecpA_.fasta "gi|354620065|gb|JN051494.1|":248-835 > ecpA.fasta
   ecpA.fasta
   
   #TODO TOMORROW: add the gene names in the fasta and merge them in a file using the following command line, make once blastn, oder make gene by gene. It is maybe clearer! find the last 3 gene sequences. At first, send the results except for gene arrangements!
   #cat sdrG.fasta gltA.fasta agrC.fasta yycG.fasta atlE.fasta psm-beta1.fasta hlb.fasta tagB.fasta capC.fasta sepA.fasta fmtC.fasta sceD.fasta SE0760.fasta esp.fasta ecpA.fasta > 15genes.fasta
   
   #makeblastdb -in HDRNA_K01.fna -dbtype nucl
   
   # -- sdrG (repeated) --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query sdrG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sdrG_on_20.blastn
   
   # -- gltA --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query gltA.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > gltA_on_20.blastn
   #-->None
   
   # -- agrC --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query agrC.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > agrC_on_20.blastn
   #-->None
   
   # -- yycG (1827 nt) --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query yycG.fasta -evalue 1e-50 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > yycG_on_20.blastn
   
   #-- atlE.fasta --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query atlE.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > atlE_on_20.blastn
   
   #-- psm-beta1.fasta --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query psm-beta1.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > psm-beta1_on_20.blastn
   
   #-- hlb.fasta --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query hlb.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > hlb_on_20.blastn
   
   #-- tagB.fasta --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query tagB.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > tagB_on_20.blastn
   
   #-- capC.fasta --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query capC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > capC_on_20.blastn
   
   #-- sepA.fasta --
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query sepA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sepA_on_20.blastn
   
   fmtC.fasta
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query fmtC.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > fmtC_on_20.blastn
   
   sceD.fasta
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query sceD.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > sceD_on_20.blastn
   
   SE0760.fasta
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query SE0760.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > SE0760_on_20.blastn
   
   esp.fasta
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query esp.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > esp_on_20.blastn
   
   ecpA.fasta
   blastn -db HDRNA_01_K01_conservative_23197.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_01.blastn
   blastn -db HDRNA_03_K01_bold_bandage_26831.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_03.blastn
   blastn -db HDRNA_06_K01_conservative_27645.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_06.blastn
   blastn -db HDRNA_07_K01_conservative_27169.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_07.blastn
   blastn -db HDRNA_08_K01_conservative_32455.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_08.blastn
   blastn -db HDRNA_12_K01_bold_37467.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_12.blastn
   blastn -db HDRNA_16_K01_conservative_37834.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_16.blastn
   blastn -db HDRNA_17_K01_conservative_37288.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_17.blastn
   blastn -db HDRNA_19_K01_bold_37377.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_19.blastn
   blastn -db HDRNA_20_K01_conservative_43457.current.gb_converted.fna -query ecpA.fasta -evalue 1e-10 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ecpA_on_20.blastn
   
   12+15+3-1=29
   
   I only found ebpS instead of ebp.
   
           #(fumC) AND "complete cds"
           gyrB: https://www.ncbi.nlm.nih.gov/nuccore/MG995415.1 Mycobacterium tuberculosis strain UKR100 GyrB (gyrB) gene, complete cds
   
           fumC: https://www.ncbi.nlm.nih.gov/nuccore/3153897
           gltA:
           icd:
   

7. Bioinformatics Tools:

   Artemis: A genome browser and annotation tool that can generate similar kinds of schematic representations.
   * GenomeDiagram from Biopython: A toolkit within Biopython that allows for the creation of high-quality genomic graphics.
   #--> https://biopython-tutorial.readthedocs.io/en/latest/notebooks/17%20-%20Graphics%20including%20GenomeDiagram.html
   IGV (Integrative Genomics Viewer): While primarily a genome browser, IGV can be used to generate snapshots that display genomic regions and variations.
   General Graphic Design Software:
   
   Adobe Illustrator: A popular graphic design tool used to create precise and detailed scientific figures.
   Inkscape: A free and open-source vector graphics editor that can be used to create diagrams like the one you've shown.
   Specialized Genomic Visualization Tools:
   
   SnapGene or Geneious: While mainly used for plasmid mapping and editing, these tools also offer features to create genomic maps and diagrams.
   MEGA (Molecular Evolutionary Genetics Analysis): Primarily used for evolutionary analyses, MEGA can also produce graphical representations of genes and genomes.
   Online Tools:
   
   PlasMapper: Used primarily for plasmid maps but can be adapted for smaller genomic regions.
   ApE (A plasmid Editor): Another tool for visualizing plasmid maps that might be used to create simplified genomic diagrams.
   Without specific information, it's hard to pinpoint exactly which one was used for your image, but it's likely that the original creator used one of the bioinformatics tools or a combination of general graphic design software to illustrate the genomic rearrangements. If you're looking to create similar images, you might want to explore some of these options to see which one best suits your needs.
   

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