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GRIL: genome rearrangement and inversion locator
Aaron E Darling1, Bob Mau, Frederick R Blattner
1Department of Computer Science, University of Wisconsin-Madison, 1656 Linden Dr, Madison, WI 53706, USA. darling@cs.wisc.edu
Bioinformatics (Oxford, England)
|December 25, 2003
Summary
GRIL is a new tool that identifies collinear regions in bacterial genomes. This facilitates multiple genome alignment and phylogenetic inference using inversion distance methods.
Area of Science:
- Genomics
- Bioinformatics
Background:
- The Genome Rearrangement Identification (GRIL) tool is available for Linux and Windows.
- GRIL is implemented in C++.
Purpose of the Study:
- To automatically identify collinear regions within bacterial-sized genome sequences.
- To provide a foundation for multiple genome alignment and phylogenetic inference.
Main Methods:
- GRIL locates regions of high sequence identity.
- User-specified criteria are used to filter these regions.
- Significant collinear regions are defined based on the filtered sequence identities.
Main Results:
- GRIL successfully identifies collinear regions across multiple genome sequences.
- The identified regions serve as input for alignment and phylogenetic analyses.
Conclusions:
- GRIL offers a computational basis for comparative genomics analyses.
- The tool supports advanced analyses like multiple genome alignment and phylogenetic inference.