ArticleBMC bioinformatics2008
GenomeMatcher: a graphical user interface for DNA sequence comparison.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers.
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Who cites it
191 citing papers in PubMed.
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- CGC1, a new reference genome forGenome research · 2025Article
- Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data.Nature communications · 2025Article
- TccP4: a novel effector identified in theMicrobiology spectrum · 2025Article
- Genome Analysis of Japanese Yersinia pseudotuberculosis Strains Isolated From Kawasaki Disease Patients and Other Sources and Their Phylogenetic Positions in the Global Y. pseudotuberculosis Population.Microbiology and immunology · 2025Article
- Genomic Insights into ProbioticMicroorganisms · 2025Article
- Dissimilatory nitrate reductions in soil Neobacillus and Bacillus strains under aerobic condition.Journal of microbiology (Seoul, Korea) · 2025Article
- Genetic Characterization of a Novel Retron Element Isolated from Vibrio mimicus.Microbiology and immunology · 2025Article
- Transcription of Nitrogen Fixation Genes Is Enhanced at Unfavorably High Oxygen Concentrations for Diazotrophic Growth in a Methane-oxidizing Bacterium.Microbes and environments · 2025Article
- Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism.Frontiers in microbiology · 2025Article
131 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe number of available genome sequences is increasing, and easy-to-use software that enables efficient comparative analysis is needed.
resultsWe 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.
conclusionGenomeMatcher 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.