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Open Access Software

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

C Titus Brown12*, Yuan Xie2, Eric H Davidson1 and R Andrew Cameron12

Author affiliations

1 Division of Biological Sciences, California Institute of Technology, Pasadena, CA 91125, USA

2 Center for Computational Regulatory Genomics, California Institute of Technology, Pasadena, CA 91125, USA

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Citation and License

BMC Bioinformatics 2005, 6:70  doi:10.1186/1471-2105-6-70

Published: 24 March 2005

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/ webcite.

Conclusion

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