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Bioinformatics Advance Access originally published online on November 3, 2005
Bioinformatics 2006 22(2):242-244; doi:10.1093/bioinformatics/bti759
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

COMPAM :visualization of combining pairwise alignments for multiple genomes

DoHoon Lee 1,2,*, Jeong-Hyeon Choi 2, Mehmet M. Dalkilic 2,3 and Sun Kim 2,3

1School of Computer Engineering, Miryang National University Miryang, Kyungnam 627-702, Korea
2School of Informatics, Indiana University—Bloomington IN 47404, USA
3Center for Genomics and Bioinformatics, Indiana University—Bloomington IN 47404, USA

*To whom correspondence should be addressed.

Summary: COMPAM is a tool for visualizing relationships among multiple whole genomes by combining all pairwise genome alignments. It displays shared conserved regions (blocks) and where these blocks occur (edges) as block relation graphs which can be explored interactively. An unannotated genome, e.g. can then be explored using information from well-annotated genomes, COG-based genome annotation and genes. COMPAM can run either as a stand-alone application or through an applet that is provided as service to PLATCOM, a toolset for whole genome comparative analysis, where a wide variety of genomes can be easily selected. Features provided by COMPAM include the ability to export genome relationship information into file formats that can be used by other existing tools.

Availability: http://bio.informatics.indiana.edu/projects/compam/

Contact: dohhlee{at}indiana.edu; sunkim2{at}indiana.edu

Received on June 3, 2005; revised on October 13, 2005; accepted on November 2, 2005

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