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Bioinformatics Advance Access originally published online on June 3, 2009
Bioinformatics 2009 25(16):2076-2077; doi:10.1093/bioinformatics/btp346
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

PROCAIN server for remote protein sequence similarity search

Yong Wang 1, Ruslan I. Sadreyev 2 and Nick V. Grishin 2,3,*

1 Biomedical Engineering Program, University of Texas Southwestern Medical Center, 2 Howard Hughes Medical Institute and 3 Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA

*To whom correspondence should be addressed.


  Abstract

Sensitive and accurate detection of distant protein homology is essential for the studies of protein structure, function and evolution. We recently developed PROCAIN, a method that is based on sequence profile comparison and involves the analysis of four signals—similarities of residue content at the profile positions combined with three types of assisting information: sequence motifs, residue conservation and predicted secondary structure. Here we present the PROCAIN web server that allows the user to submit a query sequence or multiple sequence alignment and perform the search in a profile database of choice. The output is structured similar to that of BLAST, with the list of detected homologs sorted by E-value and followed by profile–profile alignments. The front page allows the user to adjust multiple options of input processing and output formatting, as well as search settings, including the relative weights assigned to the three types of assisting information.

Availability: http://prodata.swmed.edu/procain/

Contact: grishin{at}chop.swmed.edu

Associate Editor: Burkhard Rost

Received on April 22, 2009; revised on May 28, 2009; accepted on May 29, 2009

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