CaltechAUTHORS
  A Caltech Library Service

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison

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

[img]
Preview
PDF
See Usage Policy.

323Kb

Use this Persistent URL to link to this item: http://resolver.caltech.edu/CaltechAUTHORS:BRObmcb05

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.


Item Type:Article
Additional Information:© 2005 Brown et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 18 November 2004; Accepted: 24 March 2005; Published: 24 March 2005. Authors' contributions: CTB designed and implemented the majority of the functionality described. YX implemented a significant portion of the XML-RPC functionality used for client-server interaction. EHD laid out the design requirements, aided in writing the paper, and supervised the development of FRII. RAC is responsible for running the servers and did the majority of bug testing, and also contributed to the paper. Acknowledgements: Tristan De Buysscher and Madeleine Price, under the supervision of Dr. Barbara Wold, developed the original seqcomp and contributed to FamilyRelations. Ramon Cendejas and Kevin Berney aided in the development of features and helped exercise the Cartwheel server; a complete list of contributors to FamilyRelationsII and Cartwheel can be found on the Cartwheel Web site, under Developers. We especially thank Carolina Livi, Pei-Yun Lee, Dr. Ellen Rothenberg and Dr. Erich Schwarz for extensive userinterface testing over the years. Dr. Ellen Rothenberg and Dr. Erich Schwarz both contributed significantly to discussions of new features; in addition, Sagar Damle, Tracy Teal and Dr. Erich Schwarz gave many helpful comments on this paper. We also thank two anonymous reviewers for their comments. CTB is supported by National Institutes of Health Grant GM61005, and the Beckman Institute Center for Computational Regulatory Genomics is supported by National Institutes of Health Grant RR15044.
Record Number:CaltechAUTHORS:BRObmcb05
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:BRObmcb05
Alternative URL:http://dx.doi.org/10.1186/1471-2105-6-70
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:275
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:16 May 2005
Last Modified:26 Dec 2012 08:39

Repository Staff Only: item control page