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GenomeMatcher: a graphical user interface for DNA sequence comparison.

Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M - BMC Bioinformatics (2008)

Bottom Line: GenomeMatcher images can be saved as PDF and TIFF files for presentation.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, Japan. yohtsubo@ige.tohoku.ac.jp

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.

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Example of GenomeMatcher analysis. Two sequences in the GenBank format are loaded and compared successively three times by bl2seq. Clicking the arrows besides the comparison image displays the text-based annotation information. (A) Clicking a stored image in the right image column converts it into a larger image. The black asterisks denote comparison ranges of the current image, and the red ones the ranges to be compared in the next analysis. (B) The representation of the comparison result of panel A in parallel view (parallel-flip-view, in which the upper sequence is flipped). See the instruction manual for more details.
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Figure 1: Example of GenomeMatcher analysis. Two sequences in the GenBank format are loaded and compared successively three times by bl2seq. Clicking the arrows besides the comparison image displays the text-based annotation information. (A) Clicking a stored image in the right image column converts it into a larger image. The black asterisks denote comparison ranges of the current image, and the red ones the ranges to be compared in the next analysis. (B) The representation of the comparison result of panel A in parallel view (parallel-flip-view, in which the upper sequence is flipped). See the instruction manual for more details.

Mentions: Unlike other programs, GenomeMatcher does not require a pre-computed comparison result because it compares two sequences by running programs enclosed in the application bundle or placed on user's computer. When GenomeMatcher has already been launched and two DNA sequence files have been loaded, the user can obtain a comparative image just by starting the comparison function. When blastn is used, calculation and subsequent generation of a comparative image of typical bacterial genomes finishes in a few seconds on dual 3 GHz dual-core Xeon CPUs. The examples of analysis are shown in Fig. 1.


GenomeMatcher: a graphical user interface for DNA sequence comparison.

Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M - BMC Bioinformatics (2008)

Example of GenomeMatcher analysis. Two sequences in the GenBank format are loaded and compared successively three times by bl2seq. Clicking the arrows besides the comparison image displays the text-based annotation information. (A) Clicking a stored image in the right image column converts it into a larger image. The black asterisks denote comparison ranges of the current image, and the red ones the ranges to be compared in the next analysis. (B) The representation of the comparison result of panel A in parallel view (parallel-flip-view, in which the upper sequence is flipped). See the instruction manual for more details.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553346&req=5

Figure 1: Example of GenomeMatcher analysis. Two sequences in the GenBank format are loaded and compared successively three times by bl2seq. Clicking the arrows besides the comparison image displays the text-based annotation information. (A) Clicking a stored image in the right image column converts it into a larger image. The black asterisks denote comparison ranges of the current image, and the red ones the ranges to be compared in the next analysis. (B) The representation of the comparison result of panel A in parallel view (parallel-flip-view, in which the upper sequence is flipped). See the instruction manual for more details.
Mentions: Unlike other programs, GenomeMatcher does not require a pre-computed comparison result because it compares two sequences by running programs enclosed in the application bundle or placed on user's computer. When GenomeMatcher has already been launched and two DNA sequence files have been loaded, the user can obtain a comparative image just by starting the comparison function. When blastn is used, calculation and subsequent generation of a comparative image of typical bacterial genomes finishes in a few seconds on dual 3 GHz dual-core Xeon CPUs. The examples of analysis are shown in Fig. 1.

Bottom Line: GenomeMatcher images can be saved as PDF and TIFF files for presentation.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, Japan. yohtsubo@ige.tohoku.ac.jp

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.

Show MeSH