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Bioinformatics Advance Access first published online on February 24, 2005
This version published online on March 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti350
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received October 30, 2004
Revised January 28, 2005
Accepted February 20, 2005

Applications note

PLATCOM: a Platform for Computational Comparative Genomics

Kwangmin Choi 1, Yu Ma 2, Jeong-Hyeon Choi 1, and Sun Kim 3*

1 School of Informatics, Indiana University - Bloomington, IN 47404, USA
2 Department of Computer Science, 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.
Sun Kim, E-mail: sunkim{at}bio.informatics.indiana.edu


  Abstract

Motivation: As more whole genome sequences become available, comparing multiple genomes on the sequence level can reveal insight into newbiological discovery. However, there are significant challenges for genome comparison. The challenge includes requirement for computational resources due to the large volume of genome data. More importantly, the choice of genomes to be compared is entirely subjective, so there are simply too many choices for genome comparison. For these reasons, there is pressing need for the bioinformatics systems for comparing multiple genomes where users can choose genomes to be compared freely.

Results: PLATCOM is an integrated system for the comparative analysis of multiple genomes. The system is built on several public databases and a suite of genome analysis applications are provided as exemplary genome data mining tools over these internal databases. Researchers are able to visually investigate genomic sequence similarities, conserved gene neighborhoods, conserved metabolic pathways and putative gene fusion events among a set of selected multiple genomes.

Availability: http://platcom.informatics.indiana.edu/platcom.


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