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Institut Universitaire de France (to M.T.C., N.T.T.N.); ANR [ANR-14-CE11-0006-01 to M.T.C., N.T.T.N.]; ITMO Cancer [20CM114-00 to D.T., W.S.G.]; CONACYT [11311 to A.M.R., M.P.G.]; Universidad Nacional Autonoma deMexico PAPIIT (UNAM) [IA203021]; Spanish State Research Agency, EUROPEAN REGIONAL DEVELOPMENT FUND (FEDER) [AGL2017-83358R to N.K.; AEI/FEDER, UE]; Gobierno de Aragon [A08 17R, A09 20R, Phd Contract to N.K.]; PRIMA [PCI2019-103526 to B.C.M.; Programacion Conjunta Internacional, Programa Estatal de l+D+i Orientada a los Retos de la Sociedad]; Erasmus+ (to N.K.); Norwegian Research Council [288404 to J.A.C.M.]; Institut Francais de Bioinformatique (IFB) [ANR-11-INBS-0013]; SEP-CONACYT-ECOS-ANUIES [291235 to A.M.R., M.T.C. and D.T.]. Funding for open access charge: Institut Universitaire de France.

Analysis of institutional authors

Ksouri, NajlaAuthor

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February 4, 2025
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Article

RSAT 2022: regulatory sequence analysis tools

Publicated to:Nucleic Acids Research. 50 (W1): W670-W676 - 2022-05-11 50(W1), DOI: 10.1093/nar/gkac312

Authors: Santana-Garcia, Walter; Castro-Mondragon, Jaime A; Padilla-Galvez, Monica; Nguyen, Nga Thi Thuy; Elizondo-Salas, Ana; Ksouri, Najla; Gerbes, Francois; Thieffry, Denis; Vincens, Pierre; Contreras-Moreira, Bruno; van Helden, Jacques; Thomas-Chollier, Morgane; Medina-Rivera, Alejandra

Affiliations

Aix Marseille Univ, INSERM UMR S 1090, Lab Theory & Approaches Genome Complex TAGC, F-13288 Marseille, France - Author
Estn Expt Aula Dei CSIC, Zaragoza 50059, Spain - Author
Inst Francais Bioinformat, CNRS, IFB Core, UMS 3601, Evry, France - Author
PSL Univ Paris, Inst Biol Ecole Normale Super IBENS, Ecole Normale Super, CNRS,INSERM, F-75005 Paris, France - Author
Univ Nacl Autonoma Mexico, Lab Int Invest Genoma Humano, Campus Juriquilla,Blvd Juriquilla 3001, Santiago De Queretaro 76230, Mexico - Author
Univ Oslo, Ctr Mol Med Norway NCMM, Nord EMBL Partnership, N-0318 Oslo, Norway - Author
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Abstract

RSAT (Regulatory Sequence Analysis Tools) enables the detection and the analysis of cis-regulatory elements in genomic sequences. 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/. [GRAPHICS] .

Keywords

AnimalsComputational analysisDatabaseElementsExplorationGene regulatory networksGenesGenome sequencesGenomicsRsatplants motif discoverySequence analysis, dnaSiteSize chip-seqSoftwareTranscription factors

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nucleic Acids Research due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2022, it was in position 10/285, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemistry & Molecular Biology. Notably, the journal is positioned above the 90th percentile.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 3.97. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 4.62 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 22.38 (source consulted: Dimensions Aug 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-08-03, the following number of citations:

  • WoS: 47
  • Scopus: 49
  • Europe PMC: 55

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-08-03:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 66.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 72 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 24.8.
  • The number of mentions on the social network X (formerly Twitter): 42 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: France; Mexico; Norway.