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Nucleic Acids Research 2004 32(Web Server Issue):W280-W286; doi:10.1093/nar/gkh355
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes

Ivan Ovcharenko1,2,*, Marcelo A. Nobrega3, Gabriela G. Loots1 and Lisa Stubbs1

1 Genome Biology Division and 2 Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA and 3 Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

* To whom correspondence should be addressed. Tel: +1 925 422 5035; Fax: +1 925 422 2099; Email: ovcharenko1{at}llnl.gov
Correspondence may also be addressed to Lisa Stubbs. Email: stubbs5{at}llnl.gov

Received February 11, 2004; Accepted February 25, 2004

With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have arisen. However, novel tools and strategies are required to accommodate this large volume of genomic information and to facilitate the transfer of predictions generated by comparative sequence alignment to researchers focused on experimental annotation of genome function. Here, we present the ECR Browser, a tool that provides easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences. This web-based tool (http://ecrbrowser.dcode.org) provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignments of any user-submitted sequence to the genome of choice. The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.


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