COMPAM

Visualization of combining pairwise alignments for multiple genomes

DoHoon Lee, Jeong-Hyeon Choi, Mehmet M. Dalkilic, Sun Kim

Research output: Contribution to journalArticle

6 Citations (Scopus)

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, e.g. can then be explored 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.

Original languageEnglish (US)
Pages (from-to)242-244
Number of pages3
JournalBioinformatics
Volume22
Issue number2
DOIs
StatePublished - Jan 15 2006
Externally publishedYes

Fingerprint

Pairwise
Genome
Alignment
Visualization
Genes
Molecular Sequence Annotation
Comparative Analysis
Annotation
Gene
Graph in graph theory

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

COMPAM : Visualization of combining pairwise alignments for multiple genomes. / Lee, DoHoon; Choi, Jeong-Hyeon; Dalkilic, Mehmet M.; Kim, Sun.

In: Bioinformatics, Vol. 22, No. 2, 15.01.2006, p. 242-244.

Research output: Contribution to journalArticle

Lee, DoHoon ; Choi, Jeong-Hyeon ; Dalkilic, Mehmet M. ; Kim, Sun. / COMPAM : Visualization of combining pairwise alignments for multiple genomes. In: Bioinformatics. 2006 ; Vol. 22, No. 2. pp. 242-244.
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