Software

GenomeMatcher: A graphical user interface for DNA sequence comparison

Yoshiyuki Ohtsubo^*, Wakako Ikeda-Ohtsubo, Yuji Nagata and Masataka Tsuda

• * Corresponding author: Yoshiyuki Ohtsubo yohtsubo@ige.tohoku.ac.jp

Author Affiliations

Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan

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BMC Bioinformatics 2008, 9:376 doi:10.1186/1471-2105-9-376

Published: 16 September 2008

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.

Conclusion

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.