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Nucleic Acids Research 2005 33(Web Server Issue):W56-W64; doi:10.1093/nar/gki355
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© The Author 2005. Published by Oxford University Press. All rights reserved
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 for non-commercial purposes 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. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Dcode.org anthology of comparative genomic tools

Gabriela G. Loots and Ivan Ovcharenko1,*

Genome Biology Division, Lawrence Livermore National Laboratory 7000 East Avenue, L-441 Livermore, CA 94550, USA 1Energy, Environment, Biology, and Institutional Computing Division, Lawrence Livermore National Laboratory 7000 East Avenue, L-441 Livermore, CA 94550, USA

*To whom correspondence should be addressed: Tel: +1 925 422 4723; Fax: +1 925 422 2099; Email: ovcharenko1{at}llnl.gov

Received January 11, 2005. Revised January 19, 2005. Accepted January 19, 2005.

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical application of comparative sequence analysis to genetics and genomics, we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools, zPicture and Mulan; a phylogenetic shadowing tool, eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools, rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, Creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ website.


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