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Bioinformatics Advance Access originally published online on November 7, 2006
Bioinformatics 2007 23(1):122-124; doi:10.1093/bioinformatics/btl546
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes

Gabriela Loots and Ivan Ovcharenko 1,*

CMLS 7000 East Avenue, Livermore, CA, 94550, USA
1 Computation Directorates, Lawrence Livermore National Laboratory 7000 East Avenue, Livermore, CA, 94550, USA

*To whom correspondence should be addressed.

Motivation: Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. It is freely accessible at http://ecrbase.dcode.org.

Contact: ovcharenko1{at}llnl.gov

Supplementary information: Supplementary Data are available at Bioinformatics online.

Received on September 29, 2006; revised on October 19, 2006; accepted on October 19, 2006

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