{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:21Z","timestamp":1674710421598},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Gene silencing, also called RNA interference, requires reliable assessment of silencer impacts. A critical task is to find matches between silencer oligomers and sites in the genome, in accordance with one-to-many matching rules (G\u2013U matching, with provision for mismatches). Fast search algorithms are required to support silencer impact assessments in procedures for designing effective silencer sequences.<\/jats:p>\n               <jats:p>Results: The article presents a matching algorithm and data structures specialized for matching searches, including a kernel procedure that addresses a Boolean version of the database task called the skyline search. Besides exact matches, the algorithm is extended to allow for the location-specific mismatches applicable in plants. Computational tests show that the algorithm is significantly faster than suffix-tree alternatives.<\/jats:p>\n               <jats:p>Availability: Source code, executable, data and test results are freely available at ftp:\/\/ftp.csiro.au\/Horn\/RapidMatch<\/jats:p>\n               <jats:p>Contact: \u00a0mark.horn@csiro.au<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq318","type":"journal-article","created":{"date-parts":[[2010,7,3]],"date-time":"2010-07-03T02:35:39Z","timestamp":1278124539000},"page":"1932-1937","source":"Crossref","is-referenced-by-count":3,"title":["Rapid match-searching for gene silencing assessment"],"prefix":"10.1093","volume":"26","author":[{"given":"Mark E.T.","family":"Horn","sequence":"first","affiliation":[{"name":"1 Division of Mathematics, Informatics and Statistics, CSIRO, Locked Bag 17, North Ryde NSW 1670 and 2School of Biological Sciences, University of Sydney, NSW 2006, Australia"}]},{"given":"Peter M.","family":"Waterhouse","sequence":"additional","affiliation":[{"name":"1 Division of Mathematics, Informatics and Statistics, CSIRO, Locked Bag 17, North Ryde NSW 1670 and 2School of Biological Sciences, University of Sydney, NSW 2006, Australia"}]}],"member":"286","published-online":{"date-parts":[[2010,7,2]]},"reference":[{"key":"2023012508022482300_B1","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1104\/pp.108.117275","article-title":"RNA silencing in plants: yesterday, today, and tomorrow","volume":"147","author":"Eamens","year":"2008","journal-title":"Plant Physiol."},{"key":"2023012508022482300_B2","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1038\/sj.embor.7400837","article-title":"RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway","volume":"7","author":"Fusaro","year":"2006","journal-title":"EMBO Rep."},{"key":"2023012508022482300_B3","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1093\/bioinformatics\/btk041","article-title":"GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing","volume":"22","author":"Gerlach","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012508022482300_B4","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s00778-006-0029-7","article-title":"Algorithms and analyses for maximal vector computation","volume":"16","author":"Godfrey","year":"2006","journal-title":"VLDB J."},{"key":"2023012508022482300_B5","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511574931","volume-title":"Algorithms on strings, trees and sequences: computer science and computational biology.","author":"Gusfield","year":"1997"},{"key":"2023012508022482300_B6","doi-asserted-by":"crossref","first-page":"4408","DOI":"10.1093\/bioinformatics\/bti710","article-title":"Suffix-tree analyzer (STAN): looking for nucleotidic and periodic patterns in chromosomes","volume":"21","author":"Nicolas","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508022482300_B7","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1111\/j.1365-313X.2007.03328.x","article-title":"Gene silencing in plants using artificial microRNAs and other small RNAs","volume":"53","author":"Ossowski","year":"2008","journal-title":"Plant J."},{"key":"2023012508022482300_B8","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1145\/1061318.1061320","article-title":"Progressive skyline computation in database systems","volume":"30","author":"Papadias","year":"2005","journal-title":"ACM Trans. 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Biotechnol."},{"key":"2023012508022482300_B12","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1093\/bioinformatics\/bti196","article-title":"Highly specific and accurate selection of siRNAs for high-throughput functional assays","volume":"21","author":"Santoyo","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508022482300_B13","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1105\/tpc.105.039834","article-title":"Highly specific gene silencing by artificial microRNAs in Arabidopsis","volume":"18","author":"Schwab","year":"2006","journal-title":"Plant Cell"},{"key":"2023012508022482300_B14","author":"Valin","year":"2007","journal-title":"STAN manual. 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