title: GenomeMatcher: a graphical user interface for DNA sequence comparison.
abstract: BACKGROUND
  The number of available genome sequences is increasing, and easy-to-use software that enables efficient comparative analysis is needed.
  
  
  RESULTS
  We developed GenomeMatcher, a stand-alone software package for Mac OS X. GenomeMatcher executes BLAST and MUMmer, and the detected similarities are displayed in two-dimensional and parallel views with similarity values indicated by color. Selection and re-computation of any subregions is easily performed and allows flexible and in-depth analysis. Furthermore, symbols for annotation data are displayed along the views, and the user can relate the genomic differences with annotation data. While bl2seq allows sub-Giga base comparison, three alignment programs, bl2seq, MAFFT and ClustalW, together with a dotmatch program allow comparative analysis of single-nucleotide level resolution. GenomeMatcher images can be saved as PDF and TIFF files for presentation. As examples of graphical ability of GenomeMatcher to show similarity in colors, we show two cases in Burkholderia and Vivrio strains that the nucleotide sequence of the second largest chromosome changes more rapidly than the largest chromosome.
  
  
  CONCLUSIONS
  GenomeMatcher is efficient and easy-to-use stand-alone software for in-depth comparative analysis of two sequences. GenomeMatcher is useful for detecting similarities in DNA sequences ranging in size from a few to sub-Giga bases.
authors.affiliation: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, Japan. yohtsubo@ige.tohoku.ac.jp
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Ohtsubo
authors.forename: Wakako
authors.initials: W
authors.lastname: Ikeda-Ohtsubo
authors.forename: Yuji
authors.initials: Y
authors.lastname: Nagata
authors.forename: Masataka
authors.initials: M
authors.lastname: Tsuda
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D004247:DNA
references.citation: FEMS Microbiol Lett. 1999 May 15;174(2):247-50
references.pmid: 10339815
references.citation: Mol Microbiol. 2002 Mar;43(6):1565-75
references.pmid: 11952905
references.citation: BMC Bioinformatics. 2005 Jan 17;6:9
references.pmid: 15655071
references.citation: Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
references.pmid: 12136088
references.citation: Bioinformatics. 2003 May 22;19(8):1039-40
references.pmid: 12761070
references.citation: BMC Bioinformatics. 2006 Aug 04;7:368
references.pmid: 16887044
references.citation: Bioinformatics. 2005 Aug 15;21(16):3422-3
references.pmid: 15976072
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Genome Biol. 2004;5(2):R12
references.pmid: 14759262
references.citation: BMC Bioinformatics. 2006 Oct 24;7:472
references.pmid: 17062155