Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
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
BMC Bioinformatics 2005, 6:70 doi:10.1186/1471-2105-6-70Published: 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 http://family.caltech.edu/ webcite.
These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.