{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T08:11:19Z","timestamp":1760170279970},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: RNA secondary structure analysis often requires searching for potential helices in large sequence data.<\/jats:p>\n               <jats:p>Results: We present a utility program GUUGle that efficiently locates potential helical regions under RNA base pairing rules, which include Watson\u2013Crick as well as G\u2013U pairs. It accepts a positive and a negative set of sequences, and determines all exact matches under RNA rules between positive and negative sequences that exceed a specified length. The GUUGle algorithm can also be adapted to use a precomputed suffix array of the positive sequence set. We show how this program can be effectively used as a filter preceding a more computationally expensive task such as miRNA target prediction.<\/jats:p>\n               <jats:p>Availability: GUUGle is available via the Bielefeld Bioinformatics Server at<\/jats:p>\n               <jats:p>Contact: \u00a0robert@TechFak.Uni-Bielefeld.DE<\/jats:p>","DOI":"10.1093\/bioinformatics\/btk041","type":"journal-article","created":{"date-parts":[[2006,1,11]],"date-time":"2006-01-11T01:18:22Z","timestamp":1136942302000},"page":"762-764","source":"Crossref","is-referenced-by-count":53,"title":["GUUGle: a utility for fast exact matching under RNA complementary rules including G\u2013U base pairing"],"prefix":"10.1093","volume":"22","author":[{"given":"Wolfgang","family":"Gerlach","sequence":"first","affiliation":[{"name":"Faculty of Technology, Bielefeld University \u00a0 33615 Bielefeld, Germany"}]},{"given":"Robert","family":"Giegerich","sequence":"additional","affiliation":[{"name":"Faculty of Technology, Bielefeld University \u00a0 33615 Bielefeld, Germany"}]}],"member":"286","published-online":{"date-parts":[[2006,1,10]]},"reference":[{"key":"2023012408531953100_b1","first-page":"449","article-title":"The Enhanced Suffix Array and its Applications to Genome Analysis","author":"Abouelhoda","year":"2002"},{"key":"2023012408531953100_b2","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1186\/gb-2003-5-1-r1","article-title":"MicroRNA targets in Drosophila","volume":"5","author":"Enright","year":"2003","journal-title":"Genome Biol."},{"key":"2023012408531953100_b3","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1002\/spe.535","article-title":"Efficient implementation of lazy suffix trees","volume":"33","author":"Giegerich","year":"2003","journal-title":"Software Pract. 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