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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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Comparison of two distantly located areas. The largest chromosome of B. multivorans ATCC 17616 was compared with that of B. ambifaria AMMD. (A) Starting X mode. Two white half-square rectangles indicate regions to be compared. (B) X-mode result of panel A. Exact comparison ranges are indicated.
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Figure 3: Comparison of two distantly located areas. The largest chromosome of B. multivorans ATCC 17616 was compared with that of B. ambifaria AMMD. (A) Starting X mode. Two white half-square rectangles indicate regions to be compared. (B) X-mode result of panel A. Exact comparison ranges are indicated.

Mentions: In comparative genomic analysis, traces of large-scale genomic rearrangements and insertion of large genomic islands are often observed. To analyze the configuration of the boundaries of such events, the X mode and Y mode were implemented. In these modes, the comparative results of two horizontally or vertically separated areas are displayed in close context. Upon starting either mode, selection of an area of interest by dragging generates a half-square rectangle. By clicking the image, another half-square rectangle appears, and the user sets its location. The two selected areas are compared and displayed in another window (see Fig. 3 for an example of running X mode).


GenomeMatcher: a graphical user interface for DNA sequence comparison.

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

Comparison of two distantly located areas. The largest chromosome of B. multivorans ATCC 17616 was compared with that of B. ambifaria AMMD. (A) Starting X mode. Two white half-square rectangles indicate regions to be compared. (B) X-mode result of panel A. Exact comparison ranges are indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Comparison of two distantly located areas. The largest chromosome of B. multivorans ATCC 17616 was compared with that of B. ambifaria AMMD. (A) Starting X mode. Two white half-square rectangles indicate regions to be compared. (B) X-mode result of panel A. Exact comparison ranges are indicated.
Mentions: In comparative genomic analysis, traces of large-scale genomic rearrangements and insertion of large genomic islands are often observed. To analyze the configuration of the boundaries of such events, the X mode and Y mode were implemented. In these modes, the comparative results of two horizontally or vertically separated areas are displayed in close context. Upon starting either mode, selection of an area of interest by dragging generates a half-square rectangle. By clicking the image, another half-square rectangle appears, and the user sets its location. The two selected areas are compared and displayed in another window (see Fig. 3 for an example of running X mode).

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