Genome Surveyor 2.0: cis-regulatory analysis in Drosophila

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W79-85. doi: 10.1093/nar/gkr291. Epub 2011 May 18.

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.

MeSH terms

  • Animals
  • Binding Sites
  • Drosophila / genetics
  • Drosophila melanogaster / genetics*
  • Genome, Insect*
  • Regulatory Elements, Transcriptional*
  • Software*
  • Transcription Factors / metabolism
  • User-Computer Interface

Substances

  • Transcription Factors