PLATCOM

Current status and plan for the next stages

Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, Sun Kim

Research output: Contribution to journalConference article

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.

Original languageEnglish (US)
Pages (from-to)300-304
Number of pages5
JournalLecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science)
Volume3615
StatePublished - Oct 17 2005
Externally publishedYes
EventSecond International Workshop on Data Integration in the Life Sciences, DILS 2005 - San Diego, CA, United States
Duration: Jul 20 2005Jul 22 2005

Fingerprint

Genome
Genes
Pairwise Comparisons
Data mining
Data Mining
Web-based System
Sequence Analysis
Protein Sequence
Programming
High Performance
Choose
Clustering
Proteins
Internal
Module
Prediction

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

PLATCOM : Current status and plan for the next stages. / Choi, Kwangmin; Choi, Jeong-Hyeon; Saple, Amit; Wang, Zhiping; Lee, Jason; Kim, Sun.

In: Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science), Vol. 3615, 17.10.2005, p. 300-304.

Research output: Contribution to journalConference article

Choi, Kwangmin ; Choi, Jeong-Hyeon ; Saple, Amit ; Wang, Zhiping ; Lee, Jason ; Kim, Sun. / PLATCOM : Current status and plan for the next stages. In: Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 2005 ; Vol. 3615. pp. 300-304.
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