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Vol. 20 no. 1 2004, pages 122-124
Bioinformatics © Oxford University Press 2004; all rights reserved.

Applications Note

GRIL: genome rearrangement and inversion locator

Aaron E. Darling 1,*, Bob Mau 2, Frederick R. Blattner 3 and Nicole T. Perna 2

1 Department of Computer Science and 2 Department of Animal Health and Biomedical Science, University of Wisconsin-Madison, 1656 Linden Dr, Madison, WI 53706, USA and 3 Department of Genetics, University of Wisconsin-Madison, 445 Henry Mall, Madison, WI 53706, USA

Received on February 26, 2003 ; revised on May 30, 2003 ; accepted on July 22, 2003

Summary: GRIL is a tool to automatically identify collinear regions in a set of bacterial-size genome sequences. GRIL uses three basic steps. First, regions of high sequence identity are located. Second, some of these regions are filtered based on user-specified criteria. Finally, the remaining regions of sequence identity are used to define significant collinear regions among the sequences. By locating collinear regions of sequence, GRIL provides a basis for multiple genome alignment using current alignment systems. GRIL also provides a basis for using current inversion distance tools to infer phylogeny.

Availability: GRIL is implemented in C++ and runs on any x86-based Linux or Windows platform. It is available from http://asap.ahabs.wisc.edu/gril

Supplementary information: The GRIL web site contains a detailed description of the GRIL's algorithms, an example of applying GRIL to five genomes, and verification of the correctness of the results.

Contact: darling{at}cs.wisc.edu

* To whom correspondence should be addressed.


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