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Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.
- Source :
-
BMC Bioinformatics . 2005, Vol. 6, p70-7. 7p. 3 Diagrams. - Publication Year :
- 2005
-
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. [ABSTRACT FROM AUTHOR]
- Subjects :
- *GENOMES
*BIOINFORMATICS
*GENOMICS
*ANIMAL genetics
*GRAPHICAL user interfaces
Subjects
Details
- Language :
- English
- ISSN :
- 14712105
- Volume :
- 6
- Database :
- Academic Search Index
- Journal :
- BMC Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 28833511
- Full Text :
- https://doi.org/10.1186/1471-2105-6-70