Limits...
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.

Show MeSH
Genome vs genome comparison. Total genomic sequences were compared by catenation mode. Before the comparison, DNA sequences of all replicons within a genome were concatenated. As the compared sequences are circular entities, the starting nucleotide positions and direction of sequences were adjusted to improve graphics. Parallel drawings of comparison results are shown. chr; chromosome. (A) Burkholderia multivorans ATCC 17616 vs B. ambifaria AMMD Accession numbers for ATCC 17616 are AP009385–AP009388, Accession numbers for AMMD are CP000440–CP000443(B) Vibrio vulnificus YJ016 vs V. vulnificus CMCP6 Accession numbers for YJ016 are BA000037, BA000038, and AP005352. Accession numbers for CMCP6 are AE016795 and AE016796.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2553346&req=5

Figure 2: Genome vs genome comparison. Total genomic sequences were compared by catenation mode. Before the comparison, DNA sequences of all replicons within a genome were concatenated. As the compared sequences are circular entities, the starting nucleotide positions and direction of sequences were adjusted to improve graphics. Parallel drawings of comparison results are shown. chr; chromosome. (A) Burkholderia multivorans ATCC 17616 vs B. ambifaria AMMD Accession numbers for ATCC 17616 are AP009385–AP009388, Accession numbers for AMMD are CP000440–CP000443(B) Vibrio vulnificus YJ016 vs V. vulnificus CMCP6 Accession numbers for YJ016 are BA000037, BA000038, and AP005352. Accession numbers for CMCP6 are AE016795 and AE016796.

Mentions: In another execution mode that we call catenation mode, the user can specify the individual sizes of the subregions, allowing, for example, replicon-by-replicon comparison of two multi-replicon genomes (Fig. 2AB). This mode also allows the user to compare concatenated genomes. For example, a sequence consisting of ten bacterial genomes was successfully compared to itself, thereby generating an image of reciprocal comparisons of 10 genomes in a single operation [see Additional file 1].


GenomeMatcher: a graphical user interface for DNA sequence comparison.

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

Genome vs genome comparison. Total genomic sequences were compared by catenation mode. Before the comparison, DNA sequences of all replicons within a genome were concatenated. As the compared sequences are circular entities, the starting nucleotide positions and direction of sequences were adjusted to improve graphics. Parallel drawings of comparison results are shown. chr; chromosome. (A) Burkholderia multivorans ATCC 17616 vs B. ambifaria AMMD Accession numbers for ATCC 17616 are AP009385–AP009388, Accession numbers for AMMD are CP000440–CP000443(B) Vibrio vulnificus YJ016 vs V. vulnificus CMCP6 Accession numbers for YJ016 are BA000037, BA000038, and AP005352. Accession numbers for CMCP6 are AE016795 and AE016796.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Genome vs genome comparison. Total genomic sequences were compared by catenation mode. Before the comparison, DNA sequences of all replicons within a genome were concatenated. As the compared sequences are circular entities, the starting nucleotide positions and direction of sequences were adjusted to improve graphics. Parallel drawings of comparison results are shown. chr; chromosome. (A) Burkholderia multivorans ATCC 17616 vs B. ambifaria AMMD Accession numbers for ATCC 17616 are AP009385–AP009388, Accession numbers for AMMD are CP000440–CP000443(B) Vibrio vulnificus YJ016 vs V. vulnificus CMCP6 Accession numbers for YJ016 are BA000037, BA000038, and AP005352. Accession numbers for CMCP6 are AE016795 and AE016796.
Mentions: In another execution mode that we call catenation mode, the user can specify the individual sizes of the subregions, allowing, for example, replicon-by-replicon comparison of two multi-replicon genomes (Fig. 2AB). This mode also allows the user to compare concatenated genomes. For example, a sequence consisting of ten bacterial genomes was successfully compared to itself, thereby generating an image of reciprocal comparisons of 10 genomes in a single operation [see Additional file 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