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Bioinformatics. 2015 May 1;31(9):1475-7. doi: 10.1093/bioinformatics/btu836. Epub 2014 Dec 18.

CDvist: a webserver for identification and visualization of conserved domains in protein sequences.

Author information

1
Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37861, USA and Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37861, USA and Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.

Abstract

SUMMARY:

Identification of domains in protein sequences allows their assigning to biological functions. Several webservers exist for identification of protein domains using similarity searches against various databases of protein domain models. However, none of them provides comprehensive domain coverage while allowing bulk querying and their visualization schemes can be improved. To address these issues, we developed CDvist (a comprehensive domain visualization tool), which combines the best available search algorithms and databases into a user-friendly framework. First, a given protein sequence is matched to domain models using high-specificity tools and only then unmatched segments are subjected to more sensitive algorithms resulting in a best possible comprehensive coverage. Bulk querying and rich visualization and download options provide improved functionality to domain architecture analysis.

AVAILABILITY AND IMPLEMENTATION:

Freely available on the web at http://cdvist.utk.edu

CONTACT:

oadebali@vols.utk.edu or ijouline@utk.edu.

PMID:
25527097
PMCID:
PMC4410658
DOI:
10.1093/bioinformatics/btu836
[Indexed for MEDLINE]
Free PMC Article

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