Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparisonReport as inadecuate




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BMC Bioinformatics

, 6:70

First Online: 24 March 2005Received: 18 November 2004Accepted: 24 March 2005

Abstract

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

ResultsWe 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-.

ConclusionThese tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-6-70 contains supplementary material, which is available to authorized users.

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Author: C Titus Brown - Yuan Xie - Eric H Davidson - R Andrew Cameron

Source: https://link.springer.com/







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