CGAT: A comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changesbetween closely related genomes

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Uchiyama, Ikuo ^a   Higuchi, Toshio ^b   Kobayashi, Ichizo ^c  

^a NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^b INTEC Web and Genome Informatics Corporation   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CODON USAGE BIAS; EVOLUTIONARY HISTORY; GENOME ALIGNMENT; GENOMIC SEQUENCE; MANUAL INSPECTION; SEQUENCE ANALYSIS; VISUALIZATION TOOLS; ZOOMING FUNCTION;

GENES; TOOLS;

ALIGNMENT;

CYTOSINE; GUANOSINE; BACTERIAL DNA;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENOME; CALCULATION; CODON USAGE; COMPUTER PROGRAM; EUBACTERIUM; GENE DELETION; GENE DUPLICATION; GENE INSERTION; GENE SEQUENCE; GENE TRANSLOCATION; GENETIC ANALYSIS; HELICOBACTER PYLORI; INTERSPERSED REPEAT; MOLECULAR EVOLUTION; NONHUMAN; SEQUENCE ALIGNMENT; TANDEM REPEAT; ALGORITHM; BACILLUS SUBTILIS; COMPARATIVE STUDY; COMPUTER GRAPHICS; DNA BASE COMPOSITION; DNA SEQUENCE; ESCHERICHIA COLI; GENETIC POLYMORPHISM; GENETICS; NUCLEIC ACID DATABASE; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PROCEDURES; REPRODUCIBILITY; SALMONELLA ENTERICA;

BACTERIA (MICROORGANISMS);

ALGORITHMS; BACILLUS SUBTILIS; BASE COMPOSITION; COMPUTER GRAPHICS; CONSERVED SEQUENCE; DATABASES, NUCLEIC ACID; DNA, BACTERIAL; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; HELICOBACTER PYLORI; POLYMORPHISM, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; REPRODUCIBILITY OF RESULTS; SALMONELLA ENTERICA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 33751190274     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-472     Document Type: Article

References (57)

1. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL: Alignment of whole genomes. Nucleic Acids Res 1999, 27:2369-2376.
2. Jareborg N, Birney E, Durbin R: Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res 1999, 9:815-824.
3. Kent WJ, Zahler AM: Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res 2000, 10:1115-1125.
4. Ning Z, Cox AJ, Mullikin JC: SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11:1725-1729.
5. Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
6. Ma B, Tromp J, Li M: PatternHunter: faster and more sensitive homology search. Bioinformatics 2002, 18:440-445.
7. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-107.
8. Brudno M, Chapman M, Gottgens B, Batzoglou S, Morgenstern B: Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics 2003, 4:66.
9. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003, 13:721-731.
10. Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S: Glocal alignment: finding rearrangements during alignment. Bioinformatics 2003, 19(Suppl 1):i54-62.
11. Bray N, Dubchak I, Pachter L: AVID: A global alignment program. Genome Res 2003, 13:97-102.
12. Choi JH, Cho HG, Kim S: GAME: a simple and efficient whole genome alignment method using maximal exact match filtering. Comput Biol Chem 2005, 29:244-253.
13. Huang W, Umbach DM, Li L: Accurate anchoring alignment of divergent sequences. Bioinformatics 2006, 22:29-34.
14. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W: PipMaker - a web server for aligning two genomic DNA sequences. Genome Res 2000, 10:577-586.
15. Jareborg N, Durbin R: Alfresco - a workbench for comparative genomic sequence analysis. Genome Res 2000, 10:1148-1157.
16. Yang J, Wang J, Yao ZJ, Jin Q, Shen Y, Chen R: GenomeComp: a visualization tool for microbial genome comparison. J Microbiol Methods 2003, 54:423-426.
17. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004, 32:W273-279.
18. Nix DA, Eisen MB: GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics 2005, 6:9.
19. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J: ACT: the Artemis Comparison Tool. Bioinformatics 2005, 21:3422-3423.
20. Gottgens B, Gilbert JG, Barton LM, Grafham D, Rogers J, Bentley DR, Green AR: Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res 2001, 11:87-97.
21. Dobrindt U, Hochhut B, Hentschel U, Hacker J: Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2004, 2:414-424.
22. Romero D, Palacios R: Gene amplification and genomic plasticity in prokaryotes. Annu Rev Genet 1997, 31:91-111.
23. Moran NA: Tracing the evolution of gene loss in obligate bacterial symbionts. Curr Opin Microbiol 2003, 6:512-518.
24. Nobusato A, Uchiyama I, Ohashi S, Kobayashi I: Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene 2000, 259:99-108.
25. Chinen A, Uchiyama I, Kobayashi I: Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms. Gene 2000, 259:109-121.
26. Ishikawa K, Watanabe M, Kuroita T, Uchiyama I, Bujnicki JM, Kawakami B, Tanokura M, Kobayashi I: Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi. Nucleic Acids Res 2005, 33:e112.
27. Kawai M, Uchiyama I, Koabayshi I: Genome comparison in silico in Neisseria suggests integration of filamentous bacteriophages by their own transposase. DNA Res 2005, 12:389-401.
28. Tsuru T, Kawai M, Mizutani-Ui Y, Uchiyama I, Kobayashi I: Evolution of paralogous genes: Reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus. Mol Biol Evol 2006, 23:1269-1285.
29. Kawai M, Nakao K, Uchiyama I, Kobayashi I: How genomes rearrange: Genome comparison within bacteria Neisseria suggests roles for mobile elements in formation of complex genome polymorphisms. Gene 2006, 383C:52-63.
30. Uchiyama I: MBGD: microbial genome database for comparative analysis. Nucleic Acids Res 2003, 31:58-62.
31. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
32. Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7:203-214.
33. Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85:2444-2448.
34. Delcher AL, Phillippy A, Carlton J, Salzberg SL: Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002, 30:2478-2483.
35. Gusfield D: Algorithms on strings trees and sequences Cambridge: Cambridge University Press; 1997.
36. Gilson E, Saurin W, Perrin D, Bachellier S, Hofnung M: Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Res 1991, 19:1375-1383.
37. van Belkum A, Scherer S, van Alphen L, Verbrugh H: Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 1998, 62:275-293.
38. Claverie JM, States DJ: Information enhancement methods for large scale sequence analysis. Computers Chem 1993, 17:191-201.
39. Leung MY, Blaisdell BE, Burge C, Karlin S: An efficient algorithm for identifying matches with errors in multiple long molecular sequences. J Mol Biol 1991, 221:1367-1378.
40. RepeatMasker Open-3.0 [http://www.repeatmasker.org]
41. 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.
42. GIB-IS [http://bioportal.ddbj.nig.ac.jp/is/index.html]
43. Karlin S, Mrazek J, Campbell AM: Codon usages in different gene classes of the Escherichia coli genome. Mol Microbiol 1998, 29:1341-1355.
44. Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453.
45. Uchiyama I, Higuchi T, Kobayashi I: CGAT: comparative genome analysis tool for closely related microbal genomes. In Genome Informatics 2000 Tokyo. University Academy Press; 2000:341-342.
46. Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, et al.: The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 1997, 388:539-547.
47. Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, deJonge BL, et al.: Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 1999, 397:176-180.
48. Saunders NJ, Peden JF, Hood DW, Moxon ER: Simple sequence repeats in the Helicobacter pylori genome. Mol Microbiol 1998, 27:1091-1098.
49. Levinson G, Gutman GA: Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 1987, 4:203-221.
50. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27:4636-4641.
51. Josenhans C, Eaton KA, Thevenot T, Suerbaum S: Switching of flagellar motility in Helicobacter pylori by reversible length variation of a short homopolymeric sequence repeat in fliP, a gene encoding a basal body protein. Infect Immun 2000, 68:4598-4603.
52. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, et al.: The complete genome sequence of Escherichia coli K-12. Science 1997, 277:1453-1474.
53. Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, et al.: Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 2001, 8:11-22.
54. Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, et al.: Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 2001, 413:848-852.
55. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, et al.: The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 1997, 390:249-256.
56. Takami H, Takaki Y, Chee GJ, Nishi S, Shimamura S, Suzuki H, Matsui S, Uchiyama I: Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus. Nucleic Acids Res 2004, 32:6292-6303.
57. Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5:6.