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

By Alex Bateman, Robert D. Finn. 2007

39 citations recorded by the source corpus.

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

Subfields: Molecular Biology, Spectroscopy

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Citations in the corpus

Rfam: Wikipedia, clans and the “decimal” release (2010, methodology): “These included sequence analysis based upon a SCOOP-like analysis for comparing overlapping hits from both profile hidden Markov model (HMM) and covariance model searches (18), the profile-profile comparison tool PRC (19) and literature searches for functional and evolutionary relationships.”
Protein sequence comparison and fold recognition: progress and good-practice benchmarking. (2011, methodology): “[49,50,48]).”