Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

被引：27

作者：

Brown, CT ^{[1
]}

Xie, Y

Davidson, EH

Cameron, RA

机构：

[1] CALTECH, Div Biol Sci, Pasadena, CA 91125 USA

[2] CALTECH, Ctr Computat Regulatory Genom, Pasadena, CA 91125 USA

来源：

BMC BIOINFORMATICS | 2005年 / 6卷 / 1期

关键词：

D O I：

10.1186/1471-2105-6-70

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：7

共 18 条

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