title: GRIL: genome rearrangement and inversion locator.
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.
  
  
  BACKGROUND
  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
authors.affiliation: Department of Computer Science, University of Wisconsin-Madison, 1656 Linden Dr, Madison, WI 53706, USA. darling@cs.wisc.edu
authors.forename: Aaron E
authors.initials: AE
authors.lastname: Darling
authors.forename: Bob
authors.initials: B
authors.lastname: Mau
authors.forename: Frederick R
authors.initials: FR
authors.lastname: Blattner
authors.forename: Nicole T
authors.initials: NT
authors.lastname: Perna
mesh_terms: D007446:Chromosome Inversion; D004252:DNA Mutational Analysis / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D015321:Gene Rearrangement / Q000235:genetics*; D016680:Genome, Bacterial; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software