M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.

Todd J Treangen; Xavier Messeguer

doi:10.1186/1471-2105-7-433

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M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.

Todd J Treangen·Xavier Messeguer

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Abstract

BACKGROUND: Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons. RESULTS: To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M-GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M-GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 (containing 75 cloned genomes from a set of 15 published enterobacterial genomes) in an hour. M-GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations. CONCLUSION: M-GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M-GCAT is freely available for download for academic and non-commercial use at: http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html.

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Algorithms Bacteria Base Sequence Chromosome Mapping Genome, Bacterial Molecular Sequence Data Sequence Alignment Sequence Analysis, DNA Software Species Specificity User-Computer Interface Evaluation Study Journal Article Research Support, Non-U.S. Gov't

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Todd J Treangen, Xavier Messeguer. 2006-10-05. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.. https://doi.org/10.1186/1471-2105-7-433

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