GRIL: genome rearrangement and inversion locator

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 se...

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Bibliographic Details
Published in:Bioinformatics 2004-01, Vol.20 (1), p.122-124
Main Authors: Darling, Aaron E., Mau, Bob, Blattner, Frederick R., Perna, Nicole T.
Format: Article
Language:English
Subjects:
Biological and medical sciences
Chromosome Inversion
DNA Mutational Analysis - methods
Fundamental and applied biological sciences. Psychology
Gene Expression Profiling - methods
Gene Rearrangement - genetics
General aspects
Genome, Bacterial
GRIL program
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Sequence Homology, Nucleic Acid
Software
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Description
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.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btg378