Alex Bateman1, Robert D Finn. 1. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK. agb@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 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Authors: Paul P Gardner; Jennifer Daub; John Tate; Benjamin L Moore; Isabelle H Osuch; Sam Griffiths-Jones; Robert D Finn; Eric P Nawrocki; Diana L Kolbe; Sean R Eddy; Alex Bateman Journal: Nucleic Acids Res Date: 2010-11-09 Impact factor: 16.971
Authors: Qingping Xu; Alex Bateman; Robert D Finn; Polat Abdubek; Tamara Astakhova; Herbert L Axelrod; Constantina Bakolitsa; Dennis Carlton; Connie Chen; Hsiu-Ju Chiu; Michelle Chiu; Thomas Clayton; Debanu Das; Marc C Deller; Lian Duan; Kyle Ellrott; Dustin Ernst; Carol L Farr; Julie Feuerhelm; Joanna C Grant; Anna Grzechnik; Gye Won Han; Lukasz Jaroszewski; Kevin K Jin; Heath E Klock; Mark W Knuth; Piotr Kozbial; S Sri Krishna; Abhinav Kumar; David Marciano; Daniel McMullan; Mitchell D Miller; Andrew T Morse; Edward Nigoghossian; Amanda Nopakun; Linda Okach; Christina Puckett; Ron Reyes; Christopher L Rife; Natasha Sefcovic; Henry J Tien; Christine B Trame; Henry van den Bedem; Dana Weekes; Tiffany Wooten; Keith O Hodgson; John Wooley; Marc-André Elsliger; Ashley M Deacon; Adam Godzik; Scott A Lesley; Ian A Wilson Journal: J Mol Biol Date: 2009-11-10 Impact factor: 5.469
Authors: Alex Bateman; Robert D Finn; Peter J Sims; Therese Wiedmer; Andreas Biegert; Johannes Söding Journal: Bioinformatics Date: 2008-11-13 Impact factor: 6.937