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This software suite performs (i) de novo motif discovery (including from genome-wide datasets like ChIP-seq\/ATAC-seq) (ii) genomic sequences scanning with known motifs, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations and (v) comparative genomics. RSAT comprises 50 tools. Six public Web servers (including a teaching server) are offered to meet the needs of different biological communities. RSAT philosophy and originality are: (i) a multi-modal access depending on the user needs, through web forms, command-line for local installation and programmatic web services, (ii) a support for virtually any genome (animals, bacteria, plants, totalizing over 10 000 genomes directly accessible). Since the 2018 NAR Web Software Issue, we have developed a large REST API, extended the support for additional genomes and external motif collections, enhanced some tools and Web forms, and developed a novel tool that builds or refine gene regulatory networks using motif scanning (network-interactions). The RSAT website provides extensive documentation, tutorials and published protocols. RSAT code is under open-source license and now hosted in GitHub. RSAT is available at http:\/\/www.rsat.eu\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac312","type":"journal-article","created":{"date-parts":[[2022,4,20]],"date-time":"2022-04-20T11:12:32Z","timestamp":1650453152000},"page":"W670-W676","source":"Crossref","is-referenced-by-count":95,"title":["RSAT 2022: regulatory sequence analysis tools"],"prefix":"10.1093","volume":"50","author":[{"given":"Walter","family":"Santana-Garcia","sequence":"first","affiliation":[{"name":"Institut de biologie de l\u2019Ecole normale sup\u00e9rieure (IBENS), Ecole normale sup\u00e9rieure, CNRS, INSERM, PSL Universit\u00e9 Paris , 75005 Paris, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4069-357X","authenticated-orcid":false,"given":"Jaime A","family":"Castro-Mondragon","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo , 0318 Oslo, Norway"}]},{"given":"M\u00f3nica","family":"Padilla-G\u00e1lvez","sequence":"additional","affiliation":[{"name":"Laboratorio Internacional de Investigaci\u00f3n sobre el Genoma Humano, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Campus Juriquilla, Blvd Juriquilla 3001, 76230 Santiago de Quer\u00e9taro, M\u00e9xico"}]},{"given":"Nga Thi\u00a0Thuy","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Institut de biologie de l\u2019Ecole normale sup\u00e9rieure (IBENS), Ecole normale sup\u00e9rieure, CNRS, INSERM, PSL Universit\u00e9 Paris , 75005 Paris, France"}]},{"given":"Ana","family":"Elizondo-Salas","sequence":"additional","affiliation":[{"name":"Laboratorio Internacional de Investigaci\u00f3n sobre el Genoma Humano, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Campus Juriquilla, Blvd Juriquilla 3001, 76230 Santiago de Quer\u00e9taro, M\u00e9xico"}]},{"given":"Najla","family":"Ksouri","sequence":"additional","affiliation":[{"name":"Estaci\u00f3n Experimental de Aula Dei-CSIC , 50059 Zaragoza, Spain"}]},{"given":"Fran\u00e7ois","family":"Gerbes","sequence":"additional","affiliation":[{"name":"CNRS, Institut Fran\u00e7ais de Bioinformatique , IFB-core, UMS 3601, Evry, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0271-1757","authenticated-orcid":false,"given":"Denis","family":"Thieffry","sequence":"additional","affiliation":[{"name":"Institut de biologie de l\u2019Ecole normale sup\u00e9rieure (IBENS), Ecole normale sup\u00e9rieure, CNRS, INSERM, PSL Universit\u00e9 Paris , 75005 Paris, France"}]},{"given":"Pierre","family":"Vincens","sequence":"additional","affiliation":[{"name":"Institut de biologie de l\u2019Ecole normale sup\u00e9rieure (IBENS), Ecole normale sup\u00e9rieure, CNRS, INSERM, PSL Universit\u00e9 Paris , 75005 Paris, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5462-907X","authenticated-orcid":false,"given":"Bruno","family":"Contreras-Moreira","sequence":"additional","affiliation":[{"name":"Estaci\u00f3n Experimental de Aula Dei-CSIC , 50059 Zaragoza, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8799-8584","authenticated-orcid":false,"given":"Jacques","family":"van\u00a0Helden","sequence":"additional","affiliation":[{"name":"CNRS, Institut Fran\u00e7ais de Bioinformatique , IFB-core, UMS 3601, Evry, France"},{"name":"Aix-Marseille Univ, INSERM UMR_S 1090, Lab Theory and Approaches of Genome Complexity (TAGC) , F-13288 Marseille, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2608-476X","authenticated-orcid":false,"given":"Morgane","family":"Thomas-Chollier","sequence":"additional","affiliation":[{"name":"Institut de biologie de l\u2019Ecole normale sup\u00e9rieure (IBENS), Ecole normale sup\u00e9rieure, CNRS, INSERM, PSL Universit\u00e9 Paris , 75005 Paris, France"}]},{"given":"Alejandra","family":"Medina-Rivera","sequence":"additional","affiliation":[{"name":"Laboratorio Internacional de Investigaci\u00f3n sobre el Genoma Humano, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Campus Juriquilla, Blvd Juriquilla 3001, 76230 Santiago de Quer\u00e9taro, M\u00e9xico"}]}],"member":"286","published-online":{"date-parts":[[2022,5,11]]},"reference":[{"key":"2022070423585653400_B1","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1006\/jmbi.1998.1947","article-title":"Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies","volume":"281","author":"van\u00a0Helden","year":"1998","journal-title":"J. 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