Cargando…
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...
Autores principales: | , , |
---|---|
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 |
_version_ | 1782207247951069184 |
---|---|
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. |
format | Online Article Text |
id | pubmed-3125742 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT kazemianmajid genomesurveyor20cisregulatoryanalysisindrosophila AT brodskymichaelh genomesurveyor20cisregulatoryanalysisindrosophila AT sinhasaurabh genomesurveyor20cisregulatoryanalysisindrosophila |