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RSAT: regulatory sequence analysis tools
- Source :
- Nucleic Acids Research, Nucleic Acids Research, Oxford University Press, 2008, 36, pp.W119--W127. ⟨10.1093/nar/gkn304⟩, Nucleic Acids Research, Oxford University Press, 2008, 36, pp.W119--W127, Nucleic acids research, 36 (Web Server issue
- Publication Year :
- 2008
- Publisher :
- HAL CCSD, 2008.
-
Abstract
- 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 sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). 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 (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published.<br />Journal Article<br />Research Support, Non-U.S. Gov't<br />SCOPUS: ar.j<br />info:eu-repo/semantics/published
- Subjects :
- 0106 biological sciences
Interface (Java)
[SDV]Life Sciences [q-bio]
Biology
computer.software_genre
01 natural sciences
03 medical and health sciences
User-Computer Interface
Software
Genetics
Ensembl
Pattern matching
Regulatory Elements, Transcriptional
ComputingMilieux_MISCELLANEOUS
030304 developmental biology
0303 health sciences
Internet
Software suite
Information retrieval
business.industry
Suite
Articles
Genomics
Sciences bio-médicales et agricoles
Workflow
Web service
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
business
computer
010606 plant biology & botany
Subjects
Details
- Language :
- English
- ISSN :
- 03051048 and 13624962
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research, Nucleic Acids Research, Oxford University Press, 2008, 36, pp.W119--W127. ⟨10.1093/nar/gkn304⟩, Nucleic Acids Research, Oxford University Press, 2008, 36, pp.W119--W127, Nucleic acids research, 36 (Web Server issue
- Accession number :
- edsair.doi.dedup.....1de0d2076a7a5928b8f08e0ced879407
- Full Text :
- https://doi.org/10.1093/nar/gkn304⟩