Genome surveyor 2.0: Cis-regulatory analysis in Drosophila

Majid Kazemian; Michael H. Brodsky; Saurabh Sinha

doi:10.1093/nar/gkr291

Genome surveyor 2.0: Cis-regulatory analysis in Drosophila

Majid Kazemian, Michael H. Brodsky, Saurabh Sinha

Siebel School of Computing and Data Science

Research output: Contribution to journal › Article › peer-review

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 ∼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.

Original language	English (US)
Pages (from-to)	W79-W85
Journal	Nucleic acids research
Volume	39
Issue number	SUPPL. 2
DOIs	https://doi.org/10.1093/nar/gkr291
State	Published - Jul 1 2011

ASJC Scopus subject areas

Genetics

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title = "Genome surveyor 2.0: Cis-regulatory analysis in Drosophila",

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 ∼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.",

author = "Majid Kazemian and Brodsky, {Michael H.} and Saurabh Sinha",

note = "Funding Information: Funding for open access charge: This work was supported in part by grants by the National Institute of Health (grant R01HG004744-01 to M.H.B., grant R01GM085233-01 to S.S.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.",

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doi = "10.1093/nar/gkr291",

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AU - Kazemian, Majid

AU - Brodsky, Michael H.

AU - Sinha, Saurabh

N1 - Funding Information: Funding for open access charge: This work was supported in part by grants by the National Institute of Health (grant R01HG004744-01 to M.H.B., grant R01GM085233-01 to S.S.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Genome surveyor 2.0: Cis-regulatory analysis in Drosophila

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