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Bioinformatics Advance Access published online on February 3, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm034
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© 2007 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.

SCOOP: A simple method for identification of novel protein superfamily relationships

Alex Bateman * and Robert D. Finn

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA. UK.

*To whom correspondence should be addressed. Dr. Alex Bateman, E-mail: agb{at}sanger.ac.uk


  Abstract

Motivation: Profile searches of sequence databases are a sensitive way to detect sequence relationships. Sophisticated profile-profile comparison algorithms that have been recently introduced increase search sensitivity even further.

Results: In this paper a simpler approach than profile-profile comparison is presented that has a comparable performance to state-of-the-art tools such as COMPASS, HHsearch and PRC. This approach is called SCOOP (Simple Comparison Of Outputs Program), and is shown to find known relationships between families in the Pfam database as well as detect novel distant relationships between families. Several novel discoveries are presented including the discovery that a domain of unknown function (DUF283) found in Dicer proteins is related to double-stranded RNA-binding domains.

Availability: SCOOP is freely available under a GNU GPL license from http://www.sanger.ac.uk/Users/agb/SCOOP/

Associate Editor: Alfonso Valencia

Received on October 31, 2006; revised on October 31, 2006; accepted on January 28, 2007

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