Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination.
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.
Etherington
Graham J
GJ
Department of Food Safety Science, Institute of Food Research Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK. Graham.Etherington@bbsrc.ac.uk
Dicks
Jo
J
Roberts
Ian N
IN
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
D004279:DNA, Viral