ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

Genome Biology

Volumn 12, Issue 3, 2011, Pages

  Varani, Alessandro M ^a   Siguier, Patricia ^a   Gourbeyre, Edith ^a   Charneau, Vincent ^a   Chandler, Mick ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; EUKARYOTE EVOLUTION; GENE INSERTION SEQUENCE; GENETIC DATABASE; GENETIC REGULATION; HIGH THROUGHPUT SCREENING; MATHEMATICAL ANALYSIS; METAGENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROKARYOTE; QUALITY CONTROL; WEB BROWSER; ARCHAEAL GENOME; BACTERIAL GENOME; BIOLOGY; INTERNET; METHODOLOGY; MOLECULAR GENETICS; OPEN READING FRAME; REPRODUCIBILITY; TRANSPOSON;

PROKARYOTA;

COMPUTATIONAL BIOLOGY; DNA TRANSPOSABLE ELEMENTS; GENOME, ARCHAEAL; GENOME, BACTERIAL; INTERNET; MOLECULAR SEQUENCE ANNOTATION; OPEN READING FRAMES; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 79953119888     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-3-r30     Document Type: Article

References (24)

1. Lima T, Auchincloss AH, Coudert E, Keller G, Michoud K, Rivoire C, Bulliard V, de Castro E, Lachaize C, Baratin D, Phan I, Bougueleret L, Bairoch A. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res 2009, 37:D471-478. 10.1093/nar/gkn661, 2686602, 18849571.
2. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res 2008, 18:188-196. 10.1101/gr.6743907, 2134774, 18025269.
3. Mahillon J, Chandler M. Insertion sequences. Microbiol Mol Biol Rev 1998, 62:725-774. 98933, 9729608.
4. Aziz RK, Breitbart M, Edwards RA. Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res 2010, 38:4207-4217. 10.1093/nar/gkq140, 2910039, 20215432.
5. De Palmenaer D, Vermeiren C, Mahillon J. IS231-MIC231 elements from Bacillus cereus sensu lato are modular. Mol Microbiol 2004, 53:457-467. 10.1111/j.1365-2958.2004.04146.x, 15228527.
6. Siguier P, Gagnevin L, Chandler M. The new IS1595 family, its relation to IS1 and the frontier between insertion sequences and transposons. Res Microbiol 2009, 160:232-241. 10.1016/j.resmic.2009.02.003, 19286454.
7. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006, 34:D32-36. 10.1093/nar/gkj014, 1347377, 16381877.
8. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
9. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12:1611-1618. 10.1101/gr.361602, 187536, 12368254.
10. Salzberg SL, Delcher AL, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998, 26:544-548. 10.1093/nar/26.2.544, 147303, 9421513.
11. Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 2005, 21:537-539. 10.1093/bioinformatics/bti054, 15479716.
12. Kichenaradja P, Siguier P, Perochon J, Chandler M. ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes. Nucleic Acids Res 2010, 38:D62-68. 10.1093/nar/gkp947, 2808865, 19906702.
13. Carver T, Berriman M, Tivey A, Patel C, Bohme U, Barrell BG, Parkhill J, Rajandream MA. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 2008, 24:2672-2676. 10.1093/bioinformatics/btn529, 2606163,2606163, 18845581.
14. Donlin MJ. Using the Generic Genome Browser (GBrowse). Curr Protoc Bioinformatics 2009, Chapter 9:Unit 9.9.
15. Zerillo MM, Van Sluys MA, Camargo LE, Monteiro-Vitorello CB. Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli. BMC Microbiol 2008, 8:127. 10.1186/1471-2180-8-127, 2516522, 18655699.
16. Pop M, Phillippy A, Delcher AL, Salzberg SL. Comparative genome assembly. Brief Bioinform 2004, 5:237-248. 10.1093/bib/5.3.237, 15383210.
17. Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N, Harris DE, Holden MT, Churcher CM, Bentley SD, Mungall KL, Cerdeno-Tarraga AM, Temple L, James K, Harris B, Quail MA, Achtman M, Atkin R, Baker S, Basham D, Bason N, Cherevach I, Chillingworth T, Collins M, Cronin A, Davis P, Doggett J, Feltwell T, Goble A, Hamlin N, Hauser H, et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet 2003, 35:32-40. 10.1038/ng1227, 12910271.
18. Burrus V, Waldor MK. Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 2004, 155:376-386. 10.1016/j.resmic.2004.01.012, 15207870.
19. Mazel D. Integrons: agents of bacterial evolution. Nat Rev Microbiol 2006, 4:608-620. 10.1038/nrmicro1462, 16845431.
20. ISsaga Manual. , http://issaga.biotoul.fr/ISsaga/issaga_manual.pdf
21. PHP. , http://www.php.net
22. EMBOSS. , http://emboss.sourceforge.net/
23. MySQL. , http://www.mysql.com
24. phpMyEdit. , http://www.phpmyedit.org/