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BMC Bioinformatics. 2006 Oct 5;7:433.

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

Author information

  • 1Dept. of Computer Science, Technical University of Catalonia, Barcelona, Spain. treangen@lsi.upc.edu

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.

PMID:
17022809
[PubMed - indexed for MEDLINE]
PMCID:
PMC1629028
Free PMC Article

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