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Bioinformatics Advance Access originally published online on February 24, 2005
Bioinformatics 2005 21(10):2514-2516; 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{at}oupjournals.org

PLATCOM: a Platform for Computational Comparative Genomics

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

1School of Informatics, Indiana University Bloomington, IN 47404, USA
2Department of Computer Science, Indiana University Bloomington, IN 47404, USA
3Center for Genomics and Bioinformatics, Indiana University Bloomington, IN 47404, USA

*To whom correspondence should be addressed.

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

Results: PLATCOM (Platform for Computational Comparative Genomics) 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

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


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