Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

C Titus Brown¹^,2 , Yuan Xie² , Eric H Davidson¹ and R Andrew Cameron¹^,2

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

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

author email corresponding author email

BMC Bioinformatics 2005, 6:70doi: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.