Easyfig usage

1. How to use the program?

   D: Zoom in on a ~15kb subregion at one end of the sequences
   
       Access the subregion window from the Image dropdown menu; click on file 01 and then enter 32599 and 50099 in the Min and Max "Range" boxes located directly under the list of annotation files
   
       Click (change cutoffs)
   
       Click on file 02 and then enter 1 and 15000 in the Min and Max "Range" boxes and click (change cutoffs)
   
   IMPORTANT: remember that the second Annotation file (LT2_Gifsy.gbk) has been inverted, This has been taken into account when entering the subregion range
   
       Close the subregion window with (close)
   
       Click on ( Generate blastn Files ) to generate the BLAST comparison files for these subregions (a pop-up box will ask you where you want to save the BLAST files – default is usually in the Easyfig_example1_files folder)
   
       CREATE FIGURE as described in part 1A.
   
   In the new image, the scale is still 5000 bp, but the image is zoomed in on the variable region. The minimum BLAST identity value is shown in the yellow dialog box after each figure is drawn – this can be used to calibrate the BLAST identity scale shown on the right (i.e. in this case the matches range from 100% (darkest) to 85% (lightest)).
   
   As described in the manual there are many ways to customise the image further e.g. the following list shows a few of the options available:
   
       * Feature rendering type from arrows to boxes or pointers
       * Colours of any of the features
       * Thickness of any lines
       * Height of BLAST matches
       * Height of features
       * Width of figure
       * Type of image file (bmp is default, but svg [scalable vector graphics] files can be produced by changing the file type)
       * Add a gene legend or label the genes**
   
   #https://github.com/gamcil/clinker
   - clinker to finish the last part of Data_PaulBongarts_S.epidermidis_HDRNA: namely compare gene order in the a part of genbank (        * genomic rearrangements (e.g. SCCmec deletions, ACME deletions, agr insertions)
           #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
   
   #https://mjsull.github.io/Easyfig/files.html
   #https://github.com/mjsull/Easyfig/wiki/
   Easyfig
   # - Fig. 4. AdeIJK has fewer SNPs within it and lower levels of recombination surrounding it than AdeABC or AdeFGH.
   # - In total, 100 A. baumannii genomes were aligned against reference A. baumannii AYE (NC_010410.1) and the presence of polymorphisms and recombination was determined using Gubbins.
   # - (a,c,e) Magnified parts of the genome at each ade operon, showing the levels of SNPs (red and blue squares; red are ancestral SNPs) and recombination levels (the black line on the bottom; the higher the peak the more recombination).
   # - The right-hand panels (b, d and f) show the entire genome and the position of each different ade operon, which is highlighted in red beneath the label.
   #- All panels have an associated mid-point rooted phylogenetic tree created by Snippy to show the relatedness of the A. baumannii sequences.
   #- AdeIJK (a) has fewer SNPs and recombination than AdeABC (e) and AdeFGH (c), indicating it is highly conserved.
   

2. Input Data

   https://www.genome.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1000&locale=en&serv=kegg&dbkey=genome&keywords=Acinetobacter+baumannii&page=1
   
   T00667
   aby; Acinetobacter baumannii AYE --> GCA_000069245.1_ASM6924v1
   T00660
   abm; Acinetobacter baumannii SDF --> GCA_000069205.1_ASM6920v1
   T00710
   abc; Acinetobacter baumannii ACICU --> GCA_000018445.1_ASM1844v1
   T00793
   abn; Acinetobacter baumannii AB0057 --> GCA_000021245.2_ASM2124v2
   T00795
   abb; Acinetobacter baumannii AB307-0294
   T01819
   abx; Acinetobacter baumannii 1656-2
   T01820
   abz; Acinetobacter baumannii MDR-ZJ06
   T01908
   abd; Acinetobacter baumannii TCDC-AB0715
   
   T02045
   abr; Acinetobacter baumannii MDR-TJ
   T02261
   abh; Acinetobacter baumannii TYTH-1
   T02491
   abad; Acinetobacter baumannii D1279779
   T02726
   abj; Acinetobacter baumannii BJAB07104
   
   T02727
   abab; Acinetobacter baumannii BJAB0715
   T02728
   abaj; Acinetobacter baumannii BJAB0868
   T02954
   abaz; Acinetobacter baumannii ZW85-1
   T03374
   abk; Acinetobacter baumannii AbH12O-A2
   
   T03375
   abau; Acinetobacter baumannii AB030
   T03376
   abaa; Acinetobacter baumannii AB031
   T03377
   abw; Acinetobacter baumannii AC29
   T03519
   abal; Acinetobacter baumannii LAC-4
   
   T00486
   acb; Acinetobacter baumannii ATCC 17978 --> GCA_000015425.1_ASM1542v1
   

3. After downloading the Genbank, perform the following commands to calculate the Subregions positions.

   ~/Scripts/genbank2fasta.py A.baumannii_AYE.gbk
   ~/Scripts/genbank2fasta.py A.baumannii_SDF.gbk
   ~/Scripts/genbank2fasta.py A.baumannii_ACICU.gbk
   
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_AB0057.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_AB307-0294.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_1656-2.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_MDR-ZJ06.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_TCDC-AB0715.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_MDR-TJ.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_TYTH-1.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_D1279779.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_BJAB07104.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_BJAB0715.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_BJAB0868.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_ZW85-1.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_AbH12O-A2.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_AB030.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_AB031.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_AC29.gbk
   ~/Scripts/genbank2fasta.py Acinetobacter_baumannii_LAC-4.gbk
   
   ~/Scripts/genbank2fasta.py A.baumannii_ATCC17978.gbk
   
   cat [the first 4 gbk files] Acinetobacter_baumannii_AB0057.gbk_converted.fna Acinetobacter_baumannii_AB307-0294.gbk_converted.fna Acinetobacter_baumannii_1656-2.gbk_converted.fna Acinetobacter_baumannii_MDR-ZJ06.gbk_converted.fna Acinetobacter_baumannii_TCDC-AB0715.gbk_converted.fna Acinetobacter_baumannii_MDR-TJ.gbk_converted.fna Acinetobacter_baumannii_TYTH-1.gbk_converted.fna Acinetobacter_baumannii_D1279779.gbk_converted.fna Acinetobacter_baumannii_BJAB07104.gbk_converted.fna Acinetobacter_baumannii_BJAB0715.gbk_converted.fna Acinetobacter_baumannii_BJAB0868.gbk_converted.fna Acinetobacter_baumannii_ZW85-1.gbk_converted.fna Acinetobacter_baumannii_AbH12O-A2.gbk_converted.fna Acinetobacter_baumannii_AB030.gbk_converted.fna Acinetobacter_baumannii_AB031.gbk_converted.fna Acinetobacter_baumannii_AC29.gbk_converted.fna Acinetobacter_baumannii_LAC-4.gbk_converted.fna > all_converted.fasta
   #for file in 1.easyfig.fa 2.easyfig.fa 3.easyfig.fa 4.easyfig.fa; do (cat "${file}"; echo) >> all.easyfig.fa; done
   makeblastdb -in all_converted_.fasta -dbtype nucl
   #-max_target_seqs 1
   blastn -db all_converted_.fasta -query ABAYE_RS05070.fasta -num_threads 15 -outfmt 6 -strand both -evalue 0.1 > ABAYE_RS05070_positions2.easyfig.out
   
   CU459141.1_Acinetobacter_baumannii_AYE  974325  975530 --> 964325  985530
   CU468230.2_Acinetobacter_baumannii_SDF  854002  855207 --> 844002  865207
   CP000863.1_Acinetobacter_baumannii_ACICU    2980675 2979470  --> 2969470 2990675
   CP001921.1_Acinetobacter_baumannii_1656-2   3018236 3017031 --> 3007031 to 3028236
   CP009257.1_Acinetobacter_baumannii_strain_AB030 1791300 1790095 --> 1780095 to 1801300
   CP009256.1_Acinetobacter_baumannii_strain_AB031 3303170 3301965 --> 3291965 to 3313170
   CP001182.2_Acinetobacter_baumannii_AB0057   3087319 3086114 --> 3076114 to 3097319
   CP001172.2_Acinetobacter_baumannii_AB307-0294   974367  975572 --> 964367 to 985572
   CP009534.1_Acinetobacter_baumannii_strain_AbH12O-A2 2890551 2889346 --> 2879346 to 2900551
   CP007535.2_Acinetobacter_baumannii_strain_AC29  1283600 1284805 --> 1273600 to 1294805
   CP003847.1_Acinetobacter_baumannii_BJAB0715 3060955 3059750 --> 3049750 to 3070955
   CP003849.1_Acinetobacter_baumannii_BJAB0868 2950975 2949770 --> 2939770 to 2960975
   CP003846.1_Acinetobacter_baumannii_BJAB07104    3043603 3042398 --> 3032398 to 3053603
   CP003967.2_Acinetobacter_baumannii_D1279779 2755134 2753929 --> 2743929 to 2765134
   CP007712.1_Acinetobacter_baumannii_LAC-4    976323  977528 --> 966323 to 987528
   CP003500.1_Acinetobacter_baumannii_MDR-TJ   934298  935503 --> 924298 to 945503
   CP001937.2_Acinetobacter_baumannii_MDR-ZJ06 306267  305062 --> 295062 to 316267
   CP002522.2_Acinetobacter_baumannii_TCDC-AB0715  3194910 3193705 --> 3183705 to 3204910
   CP003856.1_Acinetobacter_baumannii_TYTH-1   3248375 3247170 --> 3237170 to 3258375
   CP006768.1_Acinetobacter_baumannii_ZW85-1   921662  922867 --> 911662 to 932867
   CP000521.1_Acinetobacter_baumannii_ATCC17978    2990721 2989667 and 2944541 2944384 --> 2934384 3000721
   

4. After click the button "Generate blastn Files", manully perform the command "blastn"

   makeblastdb -in 2.easyfig.fa -dbtype nucl
   blastn -db 2.easyfig.fa -query 1.easyfig.fa -num_threads 15 -outfmt 6 -strand both -evalue 0.1 -max_target_seqs 1 > 12.easyfig.out
   makeblastdb -in 3.easyfig.fa -dbtype nucl
   blastn -db 3.easyfig.fa -query 2.easyfig.fa -num_threads 15 -outfmt 6 -strand both -evalue 0.1 -max_target_seqs 1 > 23.easyfig.out
   makeblastdb -in 4.easyfig.fa -dbtype nucl
   blastn -db 4.easyfig.fa -query 3.easyfig.fa -num_threads 15 -outfmt 6 -strand both -evalue 0.1 -max_target_seqs 1 > 34.easyfig.out
   makeblastdb -in 5.easyfig.fa -dbtype nucl
   blastn -db 5.easyfig.fa -query 4.easyfig.fa -num_threads 15 -outfmt 6 -strand both -evalue 0.1 -max_target_seqs 1 > 45.easyfig.out
   ...
   

5. Generate as an svg file, add the name of genome manually. Note that the following colors were used.

   #https://github.com/mjsull/Easyfig/wiki/Example-2.-whole-genome-comparison
   normal-minimum: aqua
   normal-maximum: blue
   inverted-minimum: orange
   inverted-maximum: red
   

6. Attachment example3_settings.easycfg

   02. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/A.baumannii_AYE.gbk    03. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/A.baumannii_SDF.gbk    04. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/A.baumannii_ACICU.gbk  05. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_1656-2.gbk 06. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_AB030.gbk  07. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_AB031.gbk  08. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_AB0057.gbk 09. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_AB307-0294.gbk 10. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_AbH12O-A2.gbk  11. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_AC29.gbk   12. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_BJAB0715.gbk   13. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_BJAB0868.gbk   14. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_BJAB07104.gbk  15. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_D1279779.gbk   16. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_LAC-4.gbk  17. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_MDR-TJ.gbk 18. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_MDR-ZJ06.gbk   19. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_TCDC-AB0715.gbk    20. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_TYTH-1.gbk 21. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/Acinetobacter_baumannii_ZW85-1.gbk 01. /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/A.baumannii_ATCC17978.gbk
   02  964325  985530  False
   03  844002  865207  False
   04  2969470 2990675 False
   05  3007031 3028236 False
   06  1780095 1801300 False
   07  3291965
       3313170 False
   08  3076114 3097319 False
   09  964367  985572  False
   10  2879346 2900551 False
   11  1273600 1294805 False
   12  3049750 3070955 False
   13  2939770 2960975 False
   14  3032398 3053603 False
   15  2743929 2765134 False
   16  966323  987528  False
   17  924298  945503  False
   18  295062  316267  False
   19  3183705 3204910 False
   20  3237170 3258375 False
   21  911662  932867  False
   01  2934384 3000721 False
   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/12.easyfig.out /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/23.easyfig.out /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/34.easyfig.out /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/45.easyfig.out /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/56.easyfig.out /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/67.easyfig.out /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/78.easyfig.out /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/89.easyfig.out /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/910.easyfig.out    /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1011.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1112.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1213.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1314.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1415.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1516.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1617.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1718.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1819.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/1920.easyfig.out   /mnt/md1/Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex/comparative_genome_plots/Easyfig_files3/2021.easyfig.out
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7. identificatio of IS (Insertion Sequence) elements

     #extracted sequence segments from the two isolates, specifically:
     #    ATCC19606: 930469 to 951674 — segment1
     #    ATCC17978: 2,934,384 to 3,000,721 — segment2
     #Then, I compared the two segments and found that positions 1-11055 of segment1 mapped to 66338-55284 of segment2, and positions 11049-21206 of segment1 mapped to 10158-23 of segment2. This means the sequence from 10159-55283 of segment2 (about 45 kb nt) is not mapped. I then extracted the 45 kb sequence (see the attached fasta file). I attempted to detect IS elements using the tool ISEScan (https://academic.oup.com/bioinformatics/article/33/21/3340/3930124). Four ISs were detected (see 45kb.fasta.xlsx; for more detailed results, see 45kb.fasta.zip).
   
     samtools faidx Acinetobacter_baumannii_ATCC19606.gbk_converted.fna CP059040.1:930469-951674 > ../ATCC19606_segment.fasta
     samtools faidx A.baumannii_ATCC17978.gbk_converted.fna CP000521.1:2934384-3000721 > ../ATCC17978_segment.fasta
     makeblastdb -in ATCC17978_segment.fasta -dbtype nucl
     blastn -db ATCC17978_segment.fasta -query ATCC19606_segment.fasta -num_threads 15 -outfmt 6 -strand both -evalue 0.1 > ATCC19606_segment_on_ATCC17978_segment.blastn
     samtools faidx ATCC17978_segment.fasta CP000521.1_2934384_3000721:10159-55283 > 45kb.fasta
   

   • ISEScan: Description: Although not a database, ISEScan is a software tool used to identify IS elements in bacterial genome sequences. It can be helpful for researchers looking to analyze newly sequenced genomes for the presence of IS elements. Website: Available on platforms like GitHub for download and integration into bioinformatics workflows.

   • TnCentral including ISFinder: Description: TnCentral is a more comprehensive resource that includes information about transposons, which are larger and more complex than simple IS elements but often contain IS sequences as part of their structure. This database provides detailed information about transposon structures, including associated genes and regulatory features.

   • ISsaga: ISsaga is a web-based tool for the identification and annotation of insertion sequences in prokaryotic genomes. It provides various features for IS element analysis, including detection, classification, and visualization. You can access ISsaga here: ISsaga (http://issaga.biotoul.fr/ISsaga/issaga_index.php)

   • ISFinder: ISFinder is a curated database and analysis platform for insertion sequences in prokaryotic genomes. It provides a comprehensive collection of IS sequences and tools for sequence analysis, classification, and annotation. You can access ISFinder here: ISFinder For ISfinder please cite: Siguier P. et al. (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34: D32-D36 (link pubmed) and the database URL (http://www-is.biotoul.fr).

   • For ISbrowser please cite: Kichenaradja P. et al. (2010) ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes. Nucleic Acids Res. 38: D62-D68 (link pubmed). For ISsaga please cite: Varani A. et al. (2011) ISsaga: an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes, Genome Biology 2011, 12:R30 (link pubmed).

   • ISMapper: ISMapper is a tool for mapping insertion sequences in bacterial genomes. It uses paired-end sequence data to identify IS element insertion sites and provides information about their genomic context. You can access ISMapper here: ISMapper ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data https://pubmed.ncbi.nlm.nih.gov/26336060/

   • ISseeker: ISseeker is a software package for the identification and annotation of insertion sequences in bacterial genomes. It provides a user-friendly interface for IS element detection and characterization. You can access ISseeker here: ISseeker

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