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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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Related in: MedlinePlus

Example of dotmatch analysis in GenomeMatcher. (A) DNA regions of CRISPR [11] in Escherichia coli K12 MG1655 genome (U00096). MG1655 genome was placed both on x- and y axes. (B) Close-up view of panel A. Exact matches with sizes larger than 'word size 1' are shown in black and those larger than 'word size 2' in red. As in the main window, regions to be compared are easily be set by dragging or pressing the navigation buttons.
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Figure 4: Example of dotmatch analysis in GenomeMatcher. (A) DNA regions of CRISPR [11] in Escherichia coli K12 MG1655 genome (U00096). MG1655 genome was placed both on x- and y axes. (B) Close-up view of panel A. Exact matches with sizes larger than 'word size 1' are shown in black and those larger than 'word size 2' in red. As in the main window, regions to be compared are easily be set by dragging or pressing the navigation buttons.

Mentions: The dotmatch program implemented in GenomeMatcher is also useful for identifying repetitive sequences. Here we show, as an example, how a CRISPR is identified in dotmatch analysis (Fig. 4).


GenomeMatcher: a graphical user interface for DNA sequence comparison.

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

Example of dotmatch analysis in GenomeMatcher. (A) DNA regions of CRISPR [11] in Escherichia coli K12 MG1655 genome (U00096). MG1655 genome was placed both on x- and y axes. (B) Close-up view of panel A. Exact matches with sizes larger than 'word size 1' are shown in black and those larger than 'word size 2' in red. As in the main window, regions to be compared are easily be set by dragging or pressing the navigation buttons.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Example of dotmatch analysis in GenomeMatcher. (A) DNA regions of CRISPR [11] in Escherichia coli K12 MG1655 genome (U00096). MG1655 genome was placed both on x- and y axes. (B) Close-up view of panel A. Exact matches with sizes larger than 'word size 1' are shown in black and those larger than 'word size 2' in red. As in the main window, regions to be compared are easily be set by dragging or pressing the navigation buttons.
Mentions: The dotmatch program implemented in GenomeMatcher is also useful for identifying repetitive sequences. Here we show, as an example, how a CRISPR is identified in dotmatch analysis (Fig. 4).

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
Related in: MedlinePlus