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Bioinformatics Advance Access published online on November 7, 2006
Bioinformatics, 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
Received September 29, 2006
Revised October 19, 2006
Accepted October 19, 2006

Applications note

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

Gabriela Loots 1 and Ivan Ovcharenko 2 *

1 CMLS, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550
2 Computation Directorates, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550

* To whom correspondence should be addressed.
Ivan Ovcharenko, E-mail: ovcharenko1{at}llnl.gov


  Abstract

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 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 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.

Associate Editor: Alfonso Valencia
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