Journal
NUCLEIC ACIDS RESEARCH
Volume 46, Issue W1, Pages W209-W214Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gky317
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Funding
- French Government by RENABI-IFB program [ANR-11-INSB-0013]
- ANR [ANR-14-CE11-0006-02]
- CONACYT [269449]
- Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica - Universidad Nacional Autonoma de Mexico (PAPIIT-UNAM) [IA206517]
- SEP-CONACYT - ECOS-ANUIES
- Ecole Doctorale des Sciences de la Vie et de la Sante
- Aix-Marseille Universite
- Norwegian Research Council [187615]
- Helse Sor-Ost
- University of Oslo through the Centre for Molecular Medicine Norway (NCMM)
- Spanish MINECO [AGL2016-80967-R]
- Aix-Marseille Universite as Chercheur Invite
- Wellcome Trust Seed Award [204562/Z/16/Z]
- PAPIIT-UNAM grant [IA200318]
- CONACYT
- Agence Nationale de la Recherche
- Wellcome Trust [204562/Z/16/Z] Funding Source: Wellcome Trust
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RSAT (Regulatory Sequence Analysis Tools) is a suite ofmodular tools for the detection and the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, including from genome-wide datasets like ChIP-seq/ATACseq, (ii) motif scanning, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations, (v) comparative genomics. Six public servers jointly support 10 000 genomes from all kingdoms. Six novel or refactored programs have been added since the 2015 NAR Web Software Issue, including updated programs to analyse regulatory variants (retrieve-variation-seq, variation-scan, convert-variations), along with tools to extract sequences from a list of coordinates (retrieve-seq-bed), to select motifs from motif collections (retrieve-matrix), and to extract orthologs based on Ensembl Compara (get-orthologs-compara). Three use cases illustrate the integration of new and refactored tools to the suite. This Anniversary update gives a 20-year perspective on the software suite. RSAT is well-documented and available through Web sites, SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services, virtual machines and stand-alone programs at http://www.rsat.eu/.
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