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Genome surveyor 2.0: cis-regulatory analysis in Drosophila

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 mo...

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Detalles Bibliográficos
Autores principales: Kazemian, Majid, Brodsky, Michael H., Sinha, Saurabh
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125742/
https://www.ncbi.nlm.nih.gov/pubmed/21593125
http://dx.doi.org/10.1093/nar/gkr291
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author Kazemian, Majid
Brodsky, Michael H.
Sinha, Saurabh
author_facet Kazemian, Majid
Brodsky, Michael H.
Sinha, Saurabh
author_sort Kazemian, Majid
collection PubMed
description 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 ∼100 to ∼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.
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spelling pubmed-31257422011-07-05 Genome surveyor 2.0: cis-regulatory analysis in Drosophila Kazemian, Majid Brodsky, Michael H. Sinha, Saurabh Nucleic Acids Res Articles 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 ∼100 to ∼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. Oxford University Press 2011-07-01 2011-05-18 /pmc/articles/PMC3125742/ /pubmed/21593125 http://dx.doi.org/10.1093/nar/gkr291 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 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.
spellingShingle Articles
Kazemian, Majid
Brodsky, Michael H.
Sinha, Saurabh
Genome surveyor 2.0: cis-regulatory analysis in Drosophila
title Genome surveyor 2.0: cis-regulatory analysis in Drosophila
title_full Genome surveyor 2.0: cis-regulatory analysis in Drosophila
title_fullStr Genome surveyor 2.0: cis-regulatory analysis in Drosophila
title_full_unstemmed Genome surveyor 2.0: cis-regulatory analysis in Drosophila
title_short Genome surveyor 2.0: cis-regulatory analysis in Drosophila
title_sort genome surveyor 2.0: cis-regulatory analysis in drosophila
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125742/
https://www.ncbi.nlm.nih.gov/pubmed/21593125
http://dx.doi.org/10.1093/nar/gkr291
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