title: Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination.
abstract: BACKGROUND
  Recombination can be a prevailing drive in shaping genome evolution. RAT (Recombination Analysis Tool) is a Java-based tool for investigating recombination events in any number of aligned sequences (protein or DNA) of any length (short viral sequences to full genomes). It is an uncomplicated and intuitive application and allows the user to view only the regions of sequence alignments they are interested in.
  
  
  RESULTS
  RAT was applied to viral sequences. Its utility was demonstrated through the detection of a known recombinant of HIV and a detailed analysis of Noroviruses, the most common cause of viral gastroenteritis in humans.
  
  
  BACKGROUND
  RAT, along with a user's guide, is freely available from http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/staff/graham_etherington/RAT.htm.
authors.affiliation: Department of Food Safety Science, Institute of Food Research Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK. Graham.Etherington@bbsrc.ac.uk
authors.forename: Graham J
authors.initials: GJ
authors.lastname: Etherington
authors.forename: Jo
authors.initials: J
authors.lastname: Dicks
authors.forename: Ian N
authors.initials: IN
authors.lastname: Roberts
mesh_terms: D004279:DNA, Viral / Q000235:genetics*; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014584:User-Computer Interface
chemical_list: D004279:DNA, Viral