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Bioinformatics Advance Access published online on August 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth500
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 28, 2004
Revised August 3, 2004
Accepted August 18, 2004

Applications note

Recombination Analysis Tool (RAT): A program for the high-throughput detection of recombination

Graham J Etherington 1*, Jo Dicks 2, Ian N Roberts 1

1 Department of Food Safety Science, Institute of Food Research, Norwich Research Park, Colney Lane, Norwich NR4 7UA, UK
2 Computational Biology Group, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK

* To whom correspondence should be addressed. E-mail: Graham.Etherington{at}bbsrc.ac.uk.


  Abstract

Motivation: 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.

Availability: RAT, along with a users guide, is freely available from: http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/staff/graham_etherington/RAT.htm.


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