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Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

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Title Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
 
Creator Brown, C. Titus
Xie, Yuan
Davidson, Eric H.
Cameron, R. Andrew
 
Subject Caltech Library Services
 
Description 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.
 
Date 2005-03-24
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://authors.library.caltech.edu/275/1/BRObmbb05.pdf
Brown, C. Titus and Xie, Yuan and Davidson, Eric H. and Cameron, R. Andrew (2005) Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison. BMC Bioinformatics, 6 (70). pp. 1-7. ISSN 1471-2105. http://resolver.caltech.edu/CaltechAUTHORS:BRObmcb05 <http://resolver.caltech.edu/CaltechAUTHORS:BRObmcb05>
 
Relation http://resolver.caltech.edu/CaltechAUTHORS:BRObmcb05
http://authors.library.caltech.edu/275/