UMMS Affiliation

Program in Gene Function and Expression; Program in Molecular Medicine

Publication Date

2011-07-01

Document Type

Article

Subjects

Transcription Factors; Enhancer Elements, Genetic; Drosophila Proteins; Regulatory Elements, Transcriptionals

Disciplines

Genetics and Genomics

Abstract

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.

Rights and Permissions

© 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.

DOI of Published Version

10.1093/nar/gkr291

Source

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W79-85. Epub 2011 May 18. Link to article on publisher's site

Journal/Book/Conference Title

Nucleic acids research

Related Resources

Link to Article in PubMed

PubMed ID

21593125

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