PLATCOM: current status and plan for the next stages

Authors:
Kwangmin Choi;Jeong-Hyeon Choi;Amit Saple;Zhiping Wang;Jason Lee;Sun Kim
Affiliations:
School of Informatics, Indiana University, IN;School of Informatics, Indiana University, IN;School of Informatics, Indiana University, IN;School of Informatics, Indiana University, IN;School of Informatics, Indiana University, IN;School of Informatics, Indiana University, IN
Venue:
DILS'05 Proceedings of the Second international conference on Data Integration in the Life Sciences
Year:
2005

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Abstract

We have been developing a web-based system for comparing multiple genomes, PLATCOM, where users can choose genomes of their choice freely and perform analysis of the selected genomes with a suite of computational tools. PLATCOM is built on internal databases such as GenBank, COG, KEGG, and Pairwise Comparison Database (PCDB) that contains all pairwise comparisons (97,034 entries) of protein sequence files (.faa) and whole genome sequence files (.fna) of 312 replicons. Since combining multiple tools for sequence analysis requires a significant amount of programming work and knowledge on each tool, we also developed and incorporated high performance sequence data mining tools such as sequence clustering and neighborhood prediction. The next plan includes defining several data types for genome analysis and integrating system modules using data mining tools that operate on the genome data types. PLATCOM is available at http://platcom.informatics.indiana.edu.