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Recently, several works demonstrated the benefits of modeling dependencies between positions within the binding site. Yet, computing the statistical significance of putative binding sites in this scenario remains a challenge.<\/jats:p>\n               <jats:p>Results: We present a general, accurate and efficient method for computing p-values of putative binding sites that is applicable to a large class of probabilistic binding site and background models. We demonstrate the accuracy of the method on synthetic and real-life data.<\/jats:p>\n               <jats:p>Availability: The procedure for scanning DNA sequences and computing the statistical significance of putative binding site scores is available upon request at http:\/\/compbio.cs.huji.ac.il\/CIS\/<\/jats:p>\n               <jats:p>Contact: \u00a0nir@cs.huji.ac.il<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti041","type":"journal-article","created":{"date-parts":[[2004,9,29]],"date-time":"2004-09-29T01:27:46Z","timestamp":1096421266000},"page":"596-600","source":"Crossref","is-referenced-by-count":21,"title":["CIS: compound importance sampling method for protein\u2013DNA binding site <i>p<\/i>-value estimation"],"prefix":"10.1093","volume":"21","author":[{"given":"Y.","family":"Barash","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"G.","family":"Elidan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"T.","family":"Kaplan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"N.","family":"Friedman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2004,9,28]]},"reference":[{"key":"2023013107212937700_B1","unstructured":"Bailey, T.L. and Gribskov, Y. 1998Combining evidence using p-values: application to sequence homology searches. 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