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Bioinformatics Advance Access published online on November 3, 2005
Bioinformatics, 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@oxfordjournals.org
Received June 3, 2005
Revised October 13, 2005
Accepted November 2, 2005

Applications note

COMPAM: visualization of combining pairwise alignments for multiple genomes

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

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

* To whom correspondence should be addressed.
DoHoon Lee, E-mail: dohhlee{at}indiana.edu; dhlee@mnu.ac.kr


  Abstract

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, for example, can then be explored by 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/.


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