Geneclusterviz: A tool for conserved gene cluster visualization, exploration and analysis

Bioinformatics

Volumn 28, Issue 11, 2012, Pages 1527-1529

  Pejaver, Vikas R ^a   An, Jaehyun ^b   Rhee, SungMin ^b   Bhan, Ankita ^c   Choi, Jeong Hyeon ^d   Liu, Boshu ^e   Lee, Heewook ^a   Brown, Pamela J ^e   Kysela, David ^e   Brun, Yves V ^e   Kim, Sun ^b  

^a INDIANA UNIVERSITY   (United States)

^b Seoul National University   (South Korea)

^c ABBOTT LABORATORIES   (United States)

^d MEDICAL COLLEGE OF GEORGIA   (United States)

^e INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

ALPHAPROTEOBACTERIA; ARTICLE; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTER PROGRAM; ESCHERICHIA COLI; GENETICS; GENOME; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE ALIGNMENT;

ALPHAPROTEOBACTERIA; CLUSTER ANALYSIS; ESCHERICHIA COLI; GENOME; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84861755032     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts177     Document Type: Article

References (12)

1. Calabrese, P.P. et al. (2003) Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics, 19(Suppl 1), i74-i80.
2. Despalins, A. et al. (2011) Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters. Bioinformatics, 27, 2905-2906.
3. Drummond, A. and Strimmer, K. (2001) PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics, 17, 662-663.
4. Eddy, S.R (1998) Profile hidden markov models. Bioinformatics, 14, 755-763.
5. Fujibuchi, W. et al. (2000) Automatic detection of conserved gene clusters in multiple genomes by graph comparison and p-quasi grouping. Nucleic Acids Res., 28, 4029-4036.
6. Haas, B.J. et al. (2004) DAGchainer: A tool for mining segmental genome duplications and synteny. Bioinformatics, 20, 3643-3646.
7. Hemmerich, C. et al. (2010) An Ergatis-based prokaryotic genome annotation web server. Bioinformatics, 26, 1122-1124.
8. Kim, S. et al. (2007) EGGS: Extraction of gene clusters by iteratively using genome context based sequence matching techniques. In Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine. IEEE Computer Society, San Jose, CA, USA, pp. 23-28.
9. Nielsen, C.B. et al. (2010) Visualizing genomes: techniques and challenges. Nat. Meth., 7, S5-S15.
10. Thompson, J.D. et al. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
11. Yang, Q. and Sze, S. (2008) Large-scale analysis of gene clustering in bacteria. Genome Res., 18, 949-956.
12. Zheng, Y. et al. (2005) Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics, 6, 243.