Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

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...

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Detalles Bibliográficos
Autores principales: Brown, C Titus, Xie, Yuan, Davidson, Eric H, Cameron, R Andrew
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087472/
https://www.ncbi.nlm.nih.gov/pubmed/15790396
http://dx.doi.org/10.1186/1471-2105-6-70
Descripción
Sumario: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 . CONCLUSION: These tools have been shown to effectively identify regulatory regions in echinoderms, mammals, and nematodes.

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