Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
CaltechAUTHORS
View Archive Info| Field | Value | |
| Title |
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
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| Creator |
Brown, C. Titus
Xie, Yuan Davidson, Eric H. Cameron, R. Andrew |
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| Subject |
Caltech Library Services
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| 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. |
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| Date |
2005-03-24
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| Type |
Article
PeerReviewed |
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| Format |
application/pdf
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| 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> |
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| Relation |
http://resolver.caltech.edu/CaltechAUTHORS:BRObmcb05
http://authors.library.caltech.edu/275/ |
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