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Resource:Regulatory Sequence Analysis Tools

Name: Resource:Regulatory Sequence Analysis Tools
Description:

The release of complete genomic sequences not only offered a huge amount of new data for the molecular biologist, but also impulsed the development of new computational techniques required for the analysis of these data.
Most informatic tools currently available were conceived essentially for the analysis of coding sequences. Non-coding sequences present however a striking interest since they govern the regulation of gene expression.
This site offers a series of tools dedicated to the detection of regulatory signals in non-coding sequences. The only input required is a list of genes of interest (e.g. a family of co-regulated genes). From this information, you can retrieve the upstream sequences over a desired distance, discover putative regulatory signals, search the matching positions for these signals in your original dataset or in whole genomes, and display the results graphically in the form of a feature map.
Abstract

The preparation of an appropriate sequence dataset is the starting point of all genomic analyses. We present retrieve-ensembl-seq, an application that considerably eases the retrieval of sequences from the Ensembl database, via our user-friendly web site or web services. The user provides Ensembl identifiers or gene names, and the program returns corresponding upstream, downstream, intronic, exonic, UTR or whole gene sequences. retrieve-ensembl-seq also offers a multiple organism mode to retrieve sequences from homologous genes at any taxonomical level. And we introduce various original filters such as the masking of coding fragments and the avoidance of sequence redundancy for genes with multiple transcripts. retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools. AVAILABILITY: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum.
Other Name(s): RSAT
Resource Type(s): Database
Resource: Resource
URL: http://rsat.ulb.ac.be/rsat/
*Id: nif-0000-31437
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to Resource:Regulatory Sequence Analysis Tools

Resource:Yeast Search for Transcriptional Regulators And Consensus Tracking

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Facts about Resource:Regulatory Sequence Analysis ToolsRDF feed
CurationStatusuncurated  +
DefiningCitationhttp://rsat.ulb.ac.be/rsat/  +
Definition

The release of complete genomic se
The release of complete genomic sequences not only offered a huge amount of new data for the molecular biologist, but also impulsed the development of new computational techniques required for the analysis of these data.
Most informatic tools currently available were conceived essentially for the analysis of coding sequences. Non-coding sequences present however a striking interest since they govern the regulation of gene expression.
This site offers a series of tools dedicated to the detection of regulatory signals in non-coding sequences. The only input required is a list of genes of interest (e.g. a family of co-regulated genes). From this information, you can retrieve the upstream sequences over a desired distance, discover putative regulatory signals, search the matching positions for these signals in your original dataset or in whole genomes, and display the results graphically in the form of a feature map.
Abstract

The preparation of an appropriate sequence dataset is the starting point of all genomic analyses. We present retrieve-ensembl-seq, an application that considerably eases the retrieval of sequences from the Ensembl database, via our user-friendly web site or web services. The user provides Ensembl identifiers or gene names, and the program returns corresponding upstream, downstream, intronic, exonic, UTR or whole gene sequences. retrieve-ensembl-seq also offers a multiple organism mode to retrieve sequences from homologous genes at any taxonomical level. And we introduce various original filters such as the masking of coding fragments and the avoidance of sequence redundancy for genes with multiple transcripts. retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools. AVAILABILITY: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum.
n be found on the RSAT public forum.
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnif-0000-31437  +
LabelResource:Regulatory Sequence Analysis Tools  +
ModifiedDate17 June 2013  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
SynonymRSAT  +