DoMosaics: Software for domain arrangement visualization and domain-centric analysis of proteins

Bioinformatics

Volumn 30, Issue 2, 2014, Pages 282-283

  Moore, Andrew D ^a   Heldy, Andreas ^a   Terrapon, Nicolas ^a   Weiner, January ^b   Bornberg Bauer, Erich ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b MAX PLANCK INSTITUTE FOR INFECTION BIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; PROTEIN;

ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; COMPUTER GRAPHICS; COMPUTER PROGRAM; DROSOPHILA MELANOGASTER; ENZYMOLOGY; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PROTEIN DOMAIN;

AMINO ACYL-TRNA SYNTHETASES; ANIMALS; COMPUTER GRAPHICS; DROSOPHILA MELANOGASTER; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS; SOFTWARE;

EID: 84892753701     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt640     Document Type: Article

References (14)

1. De Lima Morais, D.A. et al. (2011) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res., 39, D427-D434.
2. Drummond, A. and Strimmer, K. (2001) PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics, 17, 662-663.
3. Gouzy, J. et al. (1997) XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences. Comput. Appl. Biosci., 13, 601-608.
4. Griebel, T. et al. (2008) EPoS: a modular software framework for phylogenetic analysis. Bioinformatics, 24, 2399-2400.
5. Hollich, V. and Sonnhammer, E.L.L. (2007) PfamAlyzer: domain-centric homology search. Bioinformatics, 23, 3382-3383.
6. Hunter, S. et al. (2012) Interpro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40, D306-D312.
7. Lee, B. and Lee, D. (2008) DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture. Nucleic Acids Res., 36, W60-W64.
8. Moore, A.D. et al. (2013) Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree. Biochim. Biophys. Acta, 1834, 898-907.
9. Punta, M. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
10. Storm, C.E. and Sonnhammer, E.L. (2001) NIFAS: visual analysis of domain evolution in proteins. Bioinformatics, 17, 343-348.
11. Tamuri, A.U. and Laskowski, R.A. (2010) ArchSchema: a tool for interactive graphing of related Pfam domain architectures. Bioinformatics, 26, 1260-1261.
12. Terrapon, N. et al. (2009) Detection of new protein domains using co-occurrence: application to Plasmodium falciparum. Bioinformatics, 25, 3077-3083.
13. Terrapon, N. et al. (2013) Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics [Epub ahead of print, doi:10.1093/bioinformatics/btt379, July 4, 2013].
14. Wichadakul, D. et al. (2009) d-Omix: a mixer of generic protein domain analysis tools. Nucleic Acids Res., 37, W417-W421.