Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
Related Experiment Video
Updated: Aug 18, 2026

Introductory Analysis and Validation of CUT&RUN Sequencing Data
Published on: December 13, 2024
C Titus Brown1, Yuan Xie, Eric H Davidson
1Division of Biological Sciences, California Institute of Technology, Pasadena, CA 91125, USA. titus@caltech.edu
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.
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