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Genome surveyor 2.0: cis-regulatory analysis in Drosophila

dc.contributor.authorKazemian, Majid
dc.contributor.authorBrodsky, Michael H.
dc.contributor.authorSinha, Saurabh
dc.date2022-08-11T08:10:15.000
dc.date.accessioned2022-08-23T17:01:07Z
dc.date.available2022-08-23T17:01:07Z
dc.date.issued2011-07-01
dc.date.submitted2011-08-01
dc.identifier.citationNucleic Acids Res. 2011 Jul;39(Web Server issue):W79-85. Epub 2011 May 18. <a href="http://dx.doi.org/10.1093/nar/gkr291">Link to article on publisher's site</a>
dc.identifier.issn0305-1048 (Linking)
dc.identifier.doi10.1093/nar/gkr291
dc.identifier.pmid21593125
dc.identifier.urihttp://hdl.handle.net/20.500.14038/43940
dc.description.abstractGenome Surveyor 2.0 is a web-based tool for discovery and analysis of cis-regulatory elements in Drosophila, built on top of the GBrowse genome browser for convenient visualization. Genome Surveyor was developed as a tool for predicting transcription factor (TF) binding targets and cis-regulatory modules (CRMs/enhancers), based on motifs representing experimentally determined DNA binding specificities. Since its first publication, we have added substantial new functionality (e.g. phylogenetic averaging of motif scores from multiple species, and a novel CRM discovery technique), increased the number of supported motifs about 4-fold (from approximately 100 to approximately 400), added provisions for evolutionary comparison across many more Drosophila species (from 2 to 12), and improved the user-interface. The server is free and open to all users, and there is no login requirement. Address: http://veda.cs.uiuc.edu/gs.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=21593125&dopt=Abstract">Link to Article in PubMed</a>
dc.rights© The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.subjectTranscription Factors
dc.subjectEnhancer Elements, Genetic
dc.subjectDrosophila Proteins
dc.subjectRegulatory Elements, Transcriptionals
dc.subjectGenetics and Genomics
dc.titleGenome surveyor 2.0: cis-regulatory analysis in Drosophila
dc.typeJournal Article
dc.source.journaltitleNucleic acids research
dc.source.volume39
dc.source.issueWeb Server issue
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1151&amp;context=pgfe_pp&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/pgfe_pp/151
dc.identifier.contextkey2124685
refterms.dateFOA2022-08-23T17:01:08Z
html.description.abstract<p>Genome Surveyor 2.0 is a web-based tool for discovery and analysis of cis-regulatory elements in Drosophila, built on top of the GBrowse genome browser for convenient visualization. Genome Surveyor was developed as a tool for predicting transcription factor (TF) binding targets and cis-regulatory modules (CRMs/enhancers), based on motifs representing experimentally determined DNA binding specificities. Since its first publication, we have added substantial new functionality (e.g. phylogenetic averaging of motif scores from multiple species, and a novel CRM discovery technique), increased the number of supported motifs about 4-fold (from approximately 100 to approximately 400), added provisions for evolutionary comparison across many more Drosophila species (from 2 to 12), and improved the user-interface. The server is free and open to all users, and there is no login requirement. Address: http://veda.cs.uiuc.edu/gs.</p>
dc.identifier.submissionpathpgfe_pp/151
dc.contributor.departmentProgram in Molecular Medicine
dc.contributor.departmentProgram in Gene Function and Expression
dc.source.pagesW79-85


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