Geneclusterviz

A tool for conserved gene cluster visualization, exploration and analysis

Vikas R. Pejaver, Jaehyun An, SungMin Rhee, Ankita Bhan, Jeong-Hyeon Choi, Boshu Liu, Heewook Lee, Pamela J. Brown, David Kysela, Yves V. Brun, Sun Kim

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Motivation: Gene clusters are arrangements of functionally related genes on a chromosome. In bacteria, it is expected that evolutionary pressures would conserve these arrangements due to the functional advantages they provide. Visualization of conserved gene clusters across multiple genomes provides key insights into their evolutionary histories. Therefore, a software tool that enables visualization and functional analyses of gene clusters would be a great asset to the biological research community.Results: We have developed GeneclusterViz, a Java-based tool that allows for the visualization, exploration and downstream analyses of conserved gene clusters across multiple genomes. GeneclusterViz combines an easy-to-use exploration interface for gene clusters with a host of other analysis features such as multiple sequence alignments, phylogenetic analyses and integration with the KEGG pathway database.

Original languageEnglish (US)
Article numberbts177
Pages (from-to)1527-1529
Number of pages3
JournalBioinformatics
Volume28
Issue number11
DOIs
StatePublished - Jun 1 2012

Fingerprint

Multigene Family
Visualization
Genes
Gene
Genome
Arrangement
Biota
Gene Order
Sequence Alignment
Multiple Sequence Alignment
Conserve
Phylogenetics
Software Tools
Bacteria
Software
Chromosomes
Chromosome
Java
Databases
Pathway

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Geneclusterviz : A tool for conserved gene cluster visualization, exploration and analysis. / Pejaver, Vikas R.; An, Jaehyun; Rhee, SungMin; Bhan, Ankita; Choi, Jeong-Hyeon; Liu, Boshu; Lee, Heewook; Brown, Pamela J.; Kysela, David; Brun, Yves V.; Kim, Sun.

In: Bioinformatics, Vol. 28, No. 11, bts177, 01.06.2012, p. 1527-1529.

Research output: Contribution to journalArticle

Pejaver, VR, An, J, Rhee, S, Bhan, A, Choi, J-H, Liu, B, Lee, H, Brown, PJ, Kysela, D, Brun, YV & Kim, S 2012, 'Geneclusterviz: A tool for conserved gene cluster visualization, exploration and analysis', Bioinformatics, vol. 28, no. 11, bts177, pp. 1527-1529. https://doi.org/10.1093/bioinformatics/bts177
Pejaver, Vikas R. ; An, Jaehyun ; Rhee, SungMin ; Bhan, Ankita ; Choi, Jeong-Hyeon ; Liu, Boshu ; Lee, Heewook ; Brown, Pamela J. ; Kysela, David ; Brun, Yves V. ; Kim, Sun. / Geneclusterviz : A tool for conserved gene cluster visualization, exploration and analysis. In: Bioinformatics. 2012 ; Vol. 28, No. 11. pp. 1527-1529.
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