Format

Send to

Choose Destination
See comment in PubMed Commons below
BMC Bioinformatics. 2005 Mar 24;6:70.

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Author information

1
Division of Biological Sciences, California Institute of Technology, Pasadena, CA 91125, USA. titus@caltech.edu

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.

PMID:
15790396
PMCID:
PMC1087472
DOI:
10.1186/1471-2105-6-70
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Support Center