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RSAT: regulatory sequence analysis tools

M. Thomas-Chollier, O. Sand, J.-V. Turatsinze, R. Janky, M. Defrance, E. Vervisch, S. Brohee, J. van Helden
<span title="2008-05-19">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome  ...  Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features  ...  ACKNOWLEDGEMENTS The RSAT project was originated at the Universidad Nacional Autonoma de Mexico, in the laboratory of Julio Collado-Vides, to whom J.v.H. is thankful for past and present collaboration.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn304">doi:10.1093/nar/gkn304</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18495751">pmid:18495751</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2447775/">pmcid:PMC2447775</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iw7tr43q5feb3muryfinacshva">fatcat:iw7tr43q5feb3muryfinacshva</a> </span>
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RSAT 2015: Regulatory Sequence Analysis Tools

Alejandra Medina-Rivera, Matthieu Defrance, Olivier Sand, Carl Herrmann, Jaime A. Castro-Mondragon, Jeremy Delerce, Sébastien Jaeger, Christophe Blanchet, Pierre Vincens, Christophe Caron, Daniel M. Staines, Bruno Contreras-Moreira (+6 others)
<span title="2015-04-22">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences.  ...  To process large collections of peak sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict  ...  We are also thankful to the colleagues who help us to install and maintain the RSAT mirrors:  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv362">doi:10.1093/nar/gkv362</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25904632">pmid:25904632</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4489296/">pmcid:PMC4489296</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jzbr4up77jcghnkc3hzsbwdrjq">fatcat:jzbr4up77jcghnkc3hzsbwdrjq</a> </span>
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RSAT 2022: regulatory sequence analysis tools

Walter Santana-Garcia, Jaime A Castro-Mondragon, Mónica Padilla-Gálvez, Nga Thi Thuy Nguyen, Ana Elizondo-Salas, Najla Ksouri, François Gerbes, Denis Thieffry, Pierre Vincens, Bruno Contreras-Moreira, Jacques van Helden, Morgane Thomas-Chollier (+1 others)
<span title="2022-05-11">2022</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
RSAT (Regulatory Sequence Analysis Tools) enables the detection and the analysis of cis-regulatory elements in genomic sequences.  ...  , comparisons and clustering), (iv) analysis of regulatory variations and (v) comparative genomics.  ...  We also thank Olivier Sand and Matthieu Defrance for regularly answering RSAT-related questions. We thank Ieva Rauluseviciute for finding and reporting bugs in RSAT programs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkac312">doi:10.1093/nar/gkac312</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35544234">pmid:35544234</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a7cjmc2okvboxnhfwwfmyoadua">fatcat:a7cjmc2okvboxnhfwwfmyoadua</a> </span>
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RSAT 2011: regulatory sequence analysis tools

M. Thomas-Chollier, M. Defrance, A. Medina-Rivera, O. Sand, C. Herrmann, D. Thieffry, J. van Helden
<span title="2011-06-29">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
We present a pipeline called peak-motifs, integrated in the Regulatory Sequence Analysis Tools 1 , which takes as input a set of peak sequences, discovers exceptional motifs, compares them with motif databases  ...  Most existing tools present limitations on sequence size, and typically restrict motif discovery to a few hundreds peaks.  ...  We present a pipeline called peak-motifs, integrated in the Regulatory Sequence Analysis Tools 1 , which takes as input a set of peak sequences, discovers exceptional motifs, compares them with motif databases  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr377">doi:10.1093/nar/gkr377</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21715389">pmid:21715389</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3125777/">pmcid:PMC3125777</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3p3kkedccfebdlw6n7atu3veqa">fatcat:3p3kkedccfebdlw6n7atu3veqa</a> </span>
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RSAT 2018: regulatory sequence analysis tools 20th anniversary

Nga Thi Thuy Nguyen, Bruno Contreras-Moreira, Jaime A Castro-Mondragon, Walter Santana-Garcia, Raul Ossio, Carla Daniela Robles-Espinoza, Mathieu Bahin, Samuel Collombet, Pierre Vincens, Denis Thieffry, Jacques van Helden, Alejandra Medina-Rivera (+1 others)
<span title="2018-05-02">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and the analysis of cis-regulatory elements in genome sequences.  ...  ) analysis of regulatory variations, (v) comparative genomics.  ...  ACKNOWLEDGEMENTS We are particularly thankful to the colleagues who help us installing and maintaining RSAT servers: Victor del Moral Chavez, Romualdo Zayas-Lagunas, Alfredo José Hernández Alvarez (Centro  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky317">doi:10.1093/nar/gky317</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29722874">pmid:29722874</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6030903/">pmcid:PMC6030903</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hau274l2trgfhhtpxtwsqftyna">fatcat:hau274l2trgfhhtpxtwsqftyna</a> </span>
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Regulatory Sequence Analysis Tools

J. van Helden
<span title="2003-07-01">2003</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences  ...  RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank.  ...  The RSAT project was originated at the Universidad Nacional Autonoma de Mexico, in the laboratory of Julio Collado-Vides, to whom I am thankful for past and present collaboration.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg567">doi:10.1093/nar/gkg567</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12824373">pmid:12824373</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC168973/">pmcid:PMC168973</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/664jsrokcbcffkirtsydp6u46m">fatcat:664jsrokcbcffkirtsydp6u46m</a> </span>
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MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis

Kjetil Klepper, Finn Drabløs
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results: Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules.  ...  MotifLab supports comprehensive motif discovery and analysis by allowing users to integrate several popular motif discovery tools as well as different kinds of additional information, including phylogenetic  ...  The program has been designed so that users with some background in the field of regulatory sequence analysis should be able to rapidly learn how to perform standard tasks such as obtaining promoter sequences  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-9">doi:10.1186/1471-2105-14-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23323883">pmid:23323883</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3556059/">pmcid:PMC3556059</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hs4odur3anc2belv676w2trf7e">fatcat:hs4odur3anc2belv676w2trf7e</a> </span>
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RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

Morgane Thomas-Chollier, Carl Herrmann, Matthieu Defrance, Olivier Sand, Denis Thieffry, Jacques van Helden
<span title="2011-12-08">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
To our knowledge, peak-motifs is the only tool that performs a complete motif analysis and offers a user-friendly web interface without any restriction on sequence size or number of peaks.  ...  Regarding time efficiency, peakmotifs outperforms all comparable tools by several orders of magnitude.  ...  Node labels refer to the algorithm used to discover the motif: L (local-words), P (position-analysis), O (oligo-analysis), D (dyad-analysis) as well as the considered word length (6 or 7).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr1104">doi:10.1093/nar/gkr1104</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22156162">pmid:22156162</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3287167/">pmcid:PMC3287167</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uxtmsfltwngohedr6ebpgbzm6e">fatcat:uxtmsfltwngohedr6ebpgbzm6e</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3287167/PMC3287167-gkr1104.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/91/3d/913dba49bbe0a721e84fa00dde2855e736605838.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr1104"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287167" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

RSAT peak-motifs: fast extraction of transcription factor binding motifs from full-size ChIP-seq datasets

Morgane Thomas-Chollier, Matthieu Defrance, Olivier Sand, Carl Herrmann, Denis Thieffry, Jacques Van Helden
<span title="2012-02-28">2012</span> <i title="EMBnet Stichting"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/safaaq4uondrvmmn5dstg3qpp4" style="color: black;">EMBnet journal</a> </i> &nbsp;
We present a pipeline called peak-motifs, integrated in the Regulatory Sequence Analysis Tools 1 , which takes as input a set of peak sequences, discovers exceptional motifs, compares them with motif databases  ...  Most existing tools present limitations on sequence size, and typically restrict motif discovery to a few hundreds peaks.  ...  We present a pipeline called peak-motifs, integrated in the Regulatory Sequence Analysis Tools 1 , which takes as input a set of peak sequences, discovers exceptional motifs, compares them with motif databases  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14806/ej.17.b.266">doi:10.14806/ej.17.b.266</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s5cadt7h6jco7pmq4w26r3xok4">fatcat:s5cadt7h6jco7pmq4w26r3xok4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170921214019/http://journal.embnet.org/index.php/embnetjournal/article/download/266/666" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ae/d1/aed1e226bf8c2f62e303651e94479d91412661a5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14806/ej.17.b.266"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes [chapter]

Bruno Contreras-Moreira, Jaime A. Castro-Mondragon, Claire Rioualen, Carlos P. Cantalapiedra, Jacques van Helden
<span title="">2016</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
The plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu) offers specialized options for researchers dealing with plant transcriptional regulation.  ...  regulatory sequences, such as retrieving upstream sequences, motif discovery, motif comparison, pattern matching.  ...  It can be reached athttp://plants.rsat.euand also at http://floresta.eead.csic.es/rsat. On the left-side menu, select 'Sequence tools -> retrieve sequence'. 2.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-6396-6_18">doi:10.1007/978-1-4939-6396-6_18</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27557774">pmid:27557774</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fx7wjwfszra2lmsbnucd7ghnmy">fatcat:fx7wjwfszra2lmsbnucd7ghnmy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726044101/http://digital.csic.es/bitstream/10261/136253/1/Contreras-MoreiraB_MethMolBiol_2016.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c6/46/c64629ca0e0f4b820e03707effc2a750bb0b6ef2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-6396-6_18"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes [chapter]

Jaime A. Castro-Mondragon, Claire Rioualen, Bruno Contreras-Moreira, Jacques van Helden
<span title="">2016</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
The protocol starts from a set of peak coordinates (genomic regions) which can be either downloaded from ChIP-seq databases, or produced by a peak-calling software tool.  ...  position-analysis); The Plant Regulatory Sequence Analysis Tools Regulatory Sequence Analysis Tools (RSAT, http://rsat.eu/) is a specialized software suite for the analysis of cis-regulatory elements  ...  2015: Regulatory Sequence Analysis Tools.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-6396-6_19">doi:10.1007/978-1-4939-6396-6_19</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27557775">pmid:27557775</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uf4jvjkdw5ed5h4jy6bhwui3si">fatcat:uf4jvjkdw5ed5h4jy6bhwui3si</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727232517/http://digital.csic.es/bitstream/10261/136254/1/Contreras-MoreiraB_MethMolBiol-2_2016.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f8/df/f8df63f52e7d6949c4a419a81b67776328c0b275.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-6396-6_19"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding [article]

Walter Santana-Garcia, Maria Rocha-Acevedo, Lucia Ramirez, Yvon Mbouamboua, Denis Thieffry, Morgane Thomas-Chollier, Bruno Contreras-Moreira, Jacques van Helden, Alejandra Medina-Rivera
<span title="2019-04-30">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The tools are included within the well-maintained suite Regulatory Sequence Analysis Tools (RSAT, http://rsat.eu), and accessible through a web interface that currently enables analysis of five metazoa  ...  Notably, the tools support the analysis of haplotypes.  ...  Acknowledgements We thank the persons contributing to the maintenance of the RSAT  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/623090">doi:10.1101/623090</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l32csgzwhfeh5kybljuxxr6gcy">fatcat:l32csgzwhfeh5kybljuxxr6gcy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200710143040/https://www.biorxiv.org/content/biorxiv/early/2019/04/30/623090.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fb/8d/fb8de80898b8881a254766f85ca813faaa77d26b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/623090"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

RSAT Variation-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

Walter Santana-Garcia, Maria Rocha-Acevedo, Lucia Ramirez-Navarro, Yvon Mbouamboua, Denis Thieffry, Morgane Thomas-Chollier, Bruno Contreras-Moreira, Jacques van Helden, Alejandra Medina-Rivera
<span title="2019-11-07">2019</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cmflnsn2l5gylcviv447te3mku" style="color: black;">Computational and Structural Biotechnology Journal</a> </i> &nbsp;
The tools are included within the well-maintained suite Regulatory Sequence Analysis Tools (RSAT, http://rsat.eu), and accessible through a web interface that currently enables analysis of five metazoa  ...  Notably, the tools support the analysis of haplotypes.  ...  We acknowledge Salvatore Spicuglia for useful comments during the development of the tools. We thank Lambert Moyon and Swann Floc'hlay for providing feedback on the use of Variation-tools.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.csbj.2019.09.009">doi:10.1016/j.csbj.2019.09.009</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31871587">pmid:31871587</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6906655/">pmcid:PMC6906655</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z7k3s2mu5nb6zilrzdon7nvszm">fatcat:z7k3s2mu5nb6zilrzdon7nvszm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200509040343/https://digital.csic.es/bitstream/10261/197640/1/Contreras-MoreiraB_ComputatStructBiothechJ_2019.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4e/16/4e1614bafe23f03e9ae63a0aaacbc8630aad0a58.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.csbj.2019.09.009"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6906655" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections [article]

Jaime Castro-Mondragon, Sebastien Jaeger, Denis Thieffry, Morgane Thomas-Chollier, Jacques van Helden
<span title="2016-07-27">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
databases (>7,500 motifs), we show that matrix-clustering correctly groups motifs belonging to the same TF families, and can drastically reduce motif redundancy. matrix-clustering is integrated within the RSAT  ...  We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant collections of motifs.  ...  of regulatory sequences. 17/19 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/065565">doi:10.1101/065565</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jgrxzdfos5a5vhhig2pqghiqje">fatcat:jgrxzdfos5a5vhhig2pqghiqje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504133631/https://www.biorxiv.org/content/biorxiv/early/2016/12/21/065565.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a2/56/a256ea6e940598b102e32ac3f527c4c71fba2726.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/065565"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

RSAT peak-motifs: Efficient prediction of transcription factor motifs and binding sites from genome-wide sequencing peak sets

Morgane Thomas-Chollier, Matthieu Defrance, Olivier Sand, Carl Herrman, Denis Thieffry, Van Helden Jacques
<span title="2013-04-08">2013</span> <i title="EMBnet Stichting"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/safaaq4uondrvmmn5dstg3qpp4" style="color: black;">EMBnet journal</a> </i> &nbsp;
Methods The motif discovery step relies on a combination of algorithms integrated in the software suite regulatory sequence analysis tools (RSAT, http://rsat.ulb. ac.be/rsat/) (Thomas-Chollier et al.,  ...  Data sets of several tens of megabytes are processed in a few minutes on a personal computer (the most efficient tool, oligo-analysis, treats 100Mb in 3min).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14806/ej.19.a.629">doi:10.14806/ej.19.a.629</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a5rtwjcrubhqpl3n7djqahohsq">fatcat:a5rtwjcrubhqpl3n7djqahohsq</a> </span>
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