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MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for different purposes and integrated into existing workflows. It can also be used as a C++ library.<\/jats:p>\n               <jats:p>Availability: The package with documentation and examples of usage is available at http:\/\/www.cs.helsinki.fi\/group\/pssmfind. The source code is also available under the terms of a GNU General Public License (GPL).<\/jats:p>\n               <jats:p>Contact: \u00a0janne.h.korhonen@helsinki.fi<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp554","type":"journal-article","created":{"date-parts":[[2009,9,23]],"date-time":"2009-09-23T01:21:44Z","timestamp":1253668904000},"page":"3181-3182","source":"Crossref","is-referenced-by-count":193,"title":["MOODS: fast search for position weight matrix matches in DNA sequences"],"prefix":"10.1093","volume":"25","author":[{"given":"Janne","family":"Korhonen","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland and 2 Department of Information Engineering, University of Padova, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petri","family":"Martinm\u00e4ki","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland and 2 Department of Information Engineering, University of Padova, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cinzia","family":"Pizzi","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland and 2 Department of Information Engineering, University of Padova, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pasi","family":"Rastas","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland and 2 Department of Information Engineering, University of Padova, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esko","family":"Ukkonen","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland and 2 Department of Information Engineering, University of Padova, Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2009,9,22]]},"reference":[{"key":"2023013112174936600_B1","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1186\/1471-2105-7-389","article-title":"Fast index based algorithms for matching position specific scoring matrices","volume":"7","author":"Beckstette","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013112174936600_B2","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1186\/1471-2105-6-70","article-title":"Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison","volume":"6","author":"Brown","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023013112174936600_B3","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2023013112174936600_B4","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1093\/bioinformatics\/18.8.1135","article-title":"TFBS: computational framework for transcription factor binding site analysis","volume":"18","author":"Lenhard","year":"2002","journal-title":"Bioinformatics"},{"key":"2023013112174936600_B5","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1007\/978-3-642-00982-2_41","article-title":"Self-overlapping occurrences and Knuth-Morris-Pratt algorithm for weighted matching","volume-title":"Proceedings of Third International Conference on Language and Automata Theory and Applications (LATA)","author":"Liefooghe","year":"2009"},{"key":"2023013112174936600_B6","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC(R): transcriptional regulation, from patterns to profiles","volume":"31","author":"Matys","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023013112174936600_B7","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1007\/978-3-540-71233-6_19","article-title":"Fast search algorithms for position specific scoring matrices","volume-title":"Proceedings of Bioinformatics Research and Development Conference (BIRD)","author":"Pizzi","year":"2007"},{"key":"2023013112174936600_B8","article-title":"Finding significant matches of position weight matrices in linear time","author":"Pizzi","year":"2009","journal-title":"IEEE\/ACM Trans Comput. 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