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

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.

Fig. 1.

Workflow and visualization example. (a) Primary sequence is used as input and transmembrane (gray), low complexity (magenta), and coiled-coil (green) regions are predicted. (b) HMMER3 scan against Pfam database is executed and first domain architecture is built. (c–e) HHblits followed by HHsearch is executed against (c) Pfam, (d) PDB and (e) CDD databases. (f) Domain coverage option: gray background represents the whole length of model whereas red bar displays the portion of the model that aligns with the query. Square points represent the domain positions that do not align with the query. (g) Alignment option. Sequence is displayed to scale, and each bar stands for alignment quality at that position. The absence of the bar at a given position indicates gap in the alignment on query side