SCOOP: a simple method for identification of novel protein superfamily relationships.
BACKGROUND
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 article, 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.


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


BACKGROUND
Supplementary data are available at Bioinformatics online.
Bateman
Alex
A
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK. agb@sanger.ac.uk
Finn
Robert D
RD
D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D005810:Multigene Family; D010363:Pattern Recognition, Automated; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
D011506:Proteins