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Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison
C Titus Brown1, Yuan Xie, Eric H Davidson
1Division of Biological Sciences, California Institute of Technology, Pasadena, CA 91125, USA. titus@caltech.edu
BMC Bioinformatics
|March 26, 2005
Summary
New computational tools facilitate the discovery of cis-regulatory regions in animal genomes. These systems enable efficient comparative sequence analysis for identifying crucial genetic elements across diverse species.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Comparative sequence analysis is a key method for identifying cis-regulatory regions in animal genomes.
- Identifying these regulatory regions is crucial for understanding gene expression and regulation.
Purpose of the Study:
- To introduce three novel computational tools for comparative analysis of genomic regions.
- To facilitate the discovery of cis-regulatory elements in animal genomes.
Main Methods:
- Development of Paircomp for windowed, ungapped sequence comparisons.
- Implementation of FamilyRelationsII as a graphical viewer for interactive comparison exploration.
- Creation of Cartwheel as a web-based system for managing and executing comparisons.
Main Results:
- The described tools enable efficient analysis of paired BAC-sized genomic regions.
- Paircomp identifies sequence matches above a specified threshold.
- FamilyRelationsII and Cartwheel provide interactive visualization and management of comparative analyses.
Conclusions:
- The developed tools effectively identify regulatory regions in various animal taxa, including echinoderms, mammals, and nematodes.
- These bioinformatics tools enhance the process of discovering functional genomic elements.