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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



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


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 webcite.


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