GRIL: genome rearrangement and inversion locator.

by: AE Darling, B Mau, FR Blattner, NT Perna

Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 122-124.

View FullText article

DOI, HighWire, Pubmed, Hubmed

Reviews [Write a review of this article]

There are no reviews of this article

Find related articles from these CiteULike users

operon, aprasad, AaronDarling, treangen

Find related articles with these CiteULike tags

genomecomparison, genomerearrangement, master, microinversions, no-tag, nsfprop, rearrangements, synteny, tools

Abstract

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

@article{citeulike:580953, abstract = {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}, address = {Department of Computer Science, University of Wisconsin-Madison, 1656 Linden Dr, Madison, WI 53706, USA. darling@cs.wisc.edu}, author = {Darling, A. E. and Mau, B. and Blattner, F. R. and Perna, N. T. }, citeulike-article-id = {580953}, doi = {http://dx.doi.org/10.1093/bioinformatics/btg378}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {master, rearrangements}, month = {January}, number = {1}, pages = {122--124}, posted-at = {2008-03-10 02:27:27}, priority = {2}, title = {GRIL: genome rearrangement and inversion locator.}, url = {http://dx.doi.org/10.1093/bioinformatics/btg378}, volume = {20}, year = {2004} }

RIS record

TY - JOUR ID - citeulike:580953 L3 - citeulike-article-id:580953 TI - GRIL: genome rearrangement and inversion locator. JF - Bioinformatics VL - 20 IS - 1 SP - 122 EP - 124 AD - Department of Computer Science, University of Wisconsin-Madison, 1656 Linden Dr, Madison, WI 53706, USA. darling@cs.wisc.edu SN - 1367-4803 N2 - 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 KW - master KW - rearrangements AU - Darling, AE AU - Mau, B AU - Blattner, FR AU - Perna, NT PY - 2004/01/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btg378 ER -

RIS BibTeX