{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T19:08:12Z","timestamp":1777748892889,"version":"3.51.4"},"reference-count":0,"publisher":"SAGE Publications","issue":"1-2","license":[{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation"],"published-print":{"date-parts":[[2009,2]]},"abstract":"<jats:p>In this paper we describe some utilizing conditions of a recently published tool that offers two basic functions for the classical problem of discovering motifs in a set of promoter sequences. For the first it is assumed that not necessarily all of the sequences possess a common motif of given length l. In this case, CHECKPROMOTER allows an exact identification of maximal subsets of related promoters. The purpose of this program is to recognize putatively co-regulated genes. The second, CHECKMOTIF, solves the problem of checking if the given promoters have a common motif. It uses a fast approximation algorithm for which we were able to derive non-trivial low performance bounds (defined as the ratio of Hamming distance of the obtained solution to that of a theoretically best solution) for the computed outputs. Both programs use a novel weighted Hamming distance paradigm for evaluating the similarity of sets of l-mers, and we are able to compute performance bounds for the proposed motifs. A set of At promoters were used as a benchmark for a comparative test against five known tools. It could be verified that SiteSeeker significantly outperformed these tools.<\/jats:p>","DOI":"10.3233\/isb-2009-0386","type":"journal-article","created":{"date-parts":[[2019,12,2]],"date-time":"2019-12-02T22:38:18Z","timestamp":1575326298000},"page":"11-22","source":"Crossref","is-referenced-by-count":1,"title":["The SiteSeeker Motif Discovery Tool"],"prefix":"10.1177","volume":"9","author":[{"given":"Klaus","family":"Ecker","sequence":"first","affiliation":[{"name":"Russ College of Engineering and Technology, Ohio\r\t\t\t University, Athens, Ohio, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens","family":"Lichtenberg","sequence":"additional","affiliation":[{"name":"Russ College of Engineering and Technology, Ohio\r\t\t\t University, Athens, Ohio, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lonnie","family":"Welch","sequence":"additional","affiliation":[{"name":"Bioinformatics Laboratory, School of Electrical Engineering and Computer\r\t\t\t Science, Ohio University, Athens, Ohio, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2009,1,1]]},"container-title":["In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.3233\/ISB-2009-0386","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.3233\/ISB-2009-0386","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T11:50:23Z","timestamp":1777463423000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.3233\/ISB-2009-0386"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,1]]},"references-count":0,"journal-issue":{"issue":"1-2","published-print":{"date-parts":[[2009,2]]}},"alternative-id":["10.3233\/ISB-2009-0386"],"URL":"https:\/\/doi.org\/10.3233\/isb-2009-0386","relation":{},"ISSN":["1386-6338","1434-3207"],"issn-type":[{"value":"1386-6338","type":"print"},{"value":"1434-3207","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,1,1]]}}}