{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T13:35:37Z","timestamp":1761917737599},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Profile searches of sequence databases are a sensitive way to detect sequence relationships. Sophisticated profile\u2013profile comparison algorithms that have been recently introduced increase search sensitivity even further.<\/jats:p><jats:p>Results: In this article, a simpler approach than profile\u2013profile 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.<\/jats:p><jats:p>Availability: SCOOP is freely available under a GNU GPL license from http:\/\/www.sanger.ac.uk\/Users\/agb\/SCOOP\/<\/jats:p><jats:p>Contact: \u00a0agb@sanger.ac.uk<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm034","type":"journal-article","created":{"date-parts":[[2007,2,4]],"date-time":"2007-02-04T12:39:26Z","timestamp":1170592766000},"page":"809-814","source":"Crossref","is-referenced-by-count":36,"title":["SCOOP: a simple method for identification of novel protein superfamily relationships"],"prefix":"10.1093","volume":"23","author":[{"given":"Alex","family":"Bateman","sequence":"first","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK"}]},{"given":"Robert D.","family":"Finn","sequence":"additional","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK"}]}],"member":"286","published-online":{"date-parts":[[2007,2,3]]},"reference":[{"key":"2023041108144644000_","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023041108144644000_","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gkh039","article-title":"SCOP database in 2004: refinements integrate structure and sequence family data","volume":"32","author":"Andreeva","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023041108144644000_","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1093\/bioinformatics\/bth091","article-title":"COACH: profile-profile alignment of protein families using hidden Markov models","volume":"20","author":"Edgar","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041108144644000_","doi-asserted-by":"crossref","first-page":"D247","DOI":"10.1093\/nar\/gkj149","article-title":"Pfam: clans, web tools and services","volume":"34","author":"Finn","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023041108144644000_","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1006\/jmbi.1994.1104","article-title":"Hidden Markov models in computational biology","volume":"235","author":"Krogh","year":"1994","journal-title":"J. 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