BACKGROUND: Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes. RESULTS: We describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of cis-regulatory regions in animal genomes. All tools and their source code are freely available at . CONCLUSION: These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes

Brown, C Titus

Cameron, R Andrew

Davidson, Eric H

Xie, Yuan

English

PubMed

Background: Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes. 

Results: We describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of cis-regulatory regions in animal genomes. All tools and their source code are freely available at http://family.caltech.edu/. 

Conclusion: These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes

Brown, C. Titus

Davidson, Eric H.

Cameron, R. Andrew

Caltech Authors - Main

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

Abstract Background Comparative sequence analysis is an effective and increasingly common way to identify cis-regulatory regions in animal genomes. Results We describe three tools for comparative analysis of pairs of BAC-sized genomic regions. Paircomp is a tool that does windowed (ungapped) comparisons of two sequences and reports all matches above a set threshold. FamilyRelationsII is a graphical viewer for comparisons that enables interactive exploration of several different kinds of comparisons. Cartwheel is a Web site and compute-cluster management system used to execute and store comparisons for display by FamilyRelationsII. These tools are specialized for the discovery of cis-regulatory regions in animal genomes. All tools and their source code are freely available at http://family.caltech.edu/. Conclusion These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.</p

Davidson Eric H

Xie Yuan

Brown C Titus

Cameron R Andrew

Directory of Open Access Journals

BMC Bioinformatics

Springer - Publisher Connector

C Titus Brown

Yuan Xie

Eric H Davidson

R Andrew Cameron

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Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

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