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Paircomp, FamilyRelationsII and Cartwheel: Tools for Interspecific Sequence Comparison

Overview
Publisher Biomed Central
Specialty Biology
Date 2005 Mar 26
PMID 15790396
Citations 20
Authors
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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.

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