Paircomp, FamilyRelationsII and Cartwheel: Tools for interspecific sequence comparison

Charles Brown, Yuan Xie, Eric H. Davidson, R. Andrew Cameron

Research output: Contribution to journalArticle

30 Citations (Scopus)

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

Original languageEnglish (US)
Article number70
JournalBMC Bioinformatics
Volume6
DOIs
StatePublished - Mar 24 2005
Externally publishedYes

Fingerprint

Sequence Comparison
Nucleic Acid Regulatory Sequences
Genome
Comparative Analysis
Animals
Genes
Sequence Analysis
Mammals
Genomics
Websites
Display
Display devices

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

Paircomp, FamilyRelationsII and Cartwheel : Tools for interspecific sequence comparison. / Brown, Charles; Xie, Yuan; Davidson, Eric H.; Cameron, R. Andrew.

In: BMC Bioinformatics, Vol. 6, 70, 24.03.2005.

Research output: Contribution to journalArticle

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