{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T15:45:53Z","timestamp":1773330353814,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,4,3]],"date-time":"2023-04-03T00:00:00Z","timestamp":1680480000000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Seeking probabilistic motifs in a sequence is a common task to annotate putative transcription factor binding sites or other RNA\/DNA binding sites. Useful motif representations include position weight matrices (PWMs), dinucleotide PWMs (di-PWMs), and hidden Markov models (HMMs). Dinucleotide PWMs not only combine the simplicity of PWMs\u2014a matrix form and a cumulative scoring function\u2014but also incorporate dependency between adjacent positions in the motif (unlike PWMs which disregard any dependency). For instance to represent binding sites, the HOCOMOCO database provides di-PWM motifs derived from experimental data. Currently, two programs, SPRy-SARUS and MOODS, can search for occurrences of di-PWMs in sequences.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a Python package called dipwmsearch, which provides an original and efficient algorithm for this task (it first enumerates matching words for the di-PWM, and then searches these all at once in the sequence, even if the latter contains IUPAC codes). The user benefits from an easy installation via Pypi or conda, a comprehensive documentation, and executable scripts that facilitate the use of di-PWMs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>dipwmsearch is available at https:\/\/pypi.org\/project\/dipwmsearch\/ and https:\/\/gite.lirmm.fr\/rivals\/dipwmsearch\/ under Cecill license.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad141","type":"journal-article","created":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T22:36:13Z","timestamp":1680215773000},"source":"Crossref","is-referenced-by-count":3,"title":["dipwmsearch: a Python package for searching di-PWM motifs"],"prefix":"10.1093","volume":"39","author":[{"given":"Marie","family":"Mille","sequence":"first","affiliation":[{"name":"LIRMM, Univ Montpellier, CNRS , Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie","family":"Ripoll","sequence":"additional","affiliation":[{"name":"LIRMM, Univ Montpellier, CNRS , Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bastien","family":"Cazaux","sequence":"additional","affiliation":[{"name":"LIRMM, Univ Montpellier, CNRS , Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3791-3973","authenticated-orcid":false,"given":"Eric","family":"Rivals","sequence":"additional","affiliation":[{"name":"LIRMM, Univ Montpellier, CNRS , Montpellier, France"},{"name":"Institut Fran\u00e7ais de Bioinformatique, CNRS UAR 3601 , \u00c9vry, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,4,3]]},"reference":[{"key":"2023040719575740600_","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1145\/360825.360855","article-title":"Efficient string matching: an aid to bibliographic search","volume":"18","author":"Aho","year":"1975","journal-title":"Commun ACM"},{"key":"2023040719575740600_","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1186\/1471-2105-7-389","article-title":"Fast index based algorithms and software for matching position specific scoring matrices","volume":"7","author":"Beckstette","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023040719575740600_","doi-asserted-by":"crossref","first-page":"3181","DOI":"10.1093\/bioinformatics\/btp554","article-title":"MOODS: fast search for position weight matrix matches in DNA sequences","volume":"25","author":"Korhonen","year":"2009","journal-title":"Bioinformatics"},{"key":"2023040719575740600_","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1093\/bioinformatics\/btw683","article-title":"Fast motif matching revisited: high-order PWMs, SNPs and indels","volume":"33","author":"Korhonen","year":"2017","journal-title":"Bioinformatics"},{"key":"2023040719575740600_","doi-asserted-by":"crossref","first-page":"1340004","DOI":"10.1142\/S0219720013400040","article-title":"From binding motifs in chip-seq data to improved models of transcription factor binding sites","volume":"11","author":"Kulakovskiy","year":"2013","journal-title":"J Bioinform Comput Biol"},{"key":"2023040719575740600_","doi-asserted-by":"crossref","first-page":"D252","DOI":"10.1093\/nar\/gkx1106","article-title":"HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis","volume":"46","author":"Kulakovskiy","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023040719575740600_","first-page":"201","author":"Martin","year":"2018"},{"key":"2023040719575740600_","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1093\/bioinformatics\/16.1.16","article-title":"DNA binding sites: representation and 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