{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T12:33:55Z","timestamp":1742387635075},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"suppl_2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2003,9,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The problem of finding transcription factor binding sites in the upstream regions of given genes is algorithmically an interesting and challenging problem in computational biology. A degenerate pattern over a finite alphabet \u03a3 is a sequence of subsets of \u03a3. A string over IUPAC nucleic acid codes is also a degenerate pattern over \u03a3 = {A, C, G, T}, and is used as one of the major patterns modeling transcription factor binding sites in the upstream regions of genes. However, it is known that the problem of finding a degenerate pattern consistent with both positive and negative string sets is in general NP-complete. Our aim is to devise a heuristic algorithm to find a degenerate pattern which is optimal for positive and negative string sets w.r.t. a given score function.<\/jats:p>\n               <jats:p>Results: We have proposed an enumerative algorithm called SUPERPOSITION for finding optimal degenerate patterns with a pruning technique, which works with most all reasonable score functions. The performance score of the algorithm has been compared with those of other popular motif-finding algorithms YMF, MEME and AlignACE on various sets of co-regulated genes of yeast. In the computational experiment, SUPERPOSITION has outperformed the others on several gene sets.<\/jats:p>\n               <jats:p>Availability: The python script SUPERPOSITION is available at http:\/\/www.math.kyushu-u.ac.jp\/~om\/softwares.html<\/jats:p>\n               <jats:p>Contact: om@math.kyushu-u.ac.jp<\/jats:p>\n               <jats:p>*To whom correspondence should be addressed.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg1079","type":"journal-article","created":{"date-parts":[[2003,10,9]],"date-time":"2003-10-09T01:10:44Z","timestamp":1065661844000},"page":"ii206-ii214","source":"Crossref","is-referenced-by-count":13,"title":["Finding optimal degenerate patterns in DNA sequences"],"prefix":"10.1093","volume":"19","author":[{"given":"Daisuke","family":"Shinozaki","sequence":"first","affiliation":[]},{"given":"Tatsuya","family":"Akutsu","sequence":"additional","affiliation":[]},{"given":"Osamu","family":"Maruyama","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2003,9,27]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_2\/ii206\/180586","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_2\/ii206\/180586","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:18:43Z","timestamp":1674670723000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_2\/ii206\/180586"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,9,27]]},"references-count":0,"journal-issue":{"issue":"suppl_2","published-print":{"date-parts":[[2003,9,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg1079","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2003,9,27]]},"published":{"date-parts":[[2003,9,27]]}}}