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Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination
Graham J Etherington1, Jo Dicks, Ian N Roberts
1Department of Food Safety Science, Institute of Food Research Norwich Research Park, Colney Lane, Norwich NR4 7HA, UK. Graham.Etherington@bbsrc.ac.uk
Bioinformatics (Oxford, England)
|August 31, 2004
Summary
Recombination Analysis Tool (RAT) aids genome evolution studies by detecting recombination events in DNA or protein sequences. This intuitive Java tool was successfully applied to viral sequences, including HIV and Norovirus.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- Recombination is a significant driver of genome evolution.
- The Recombination Analysis Tool (RAT) is a Java-based application for analyzing recombination in aligned sequences.
- RAT offers an intuitive interface for users to focus on specific regions of interest within sequence alignments.
Purpose of the Study:
- To introduce and demonstrate the utility of the Recombination Analysis Tool (RAT).
- To provide a user-friendly tool for investigating recombination events across diverse sequence types and lengths.
Main Methods:
- Application of the Recombination Analysis Tool (RAT) to viral sequence data.
- Utilizing RAT's capabilities for detecting recombination events in aligned DNA and protein sequences.
Main Results:
- Demonstrated RAT's effectiveness in identifying a known HIV recombinant.
- Conducted a detailed analysis of Noroviruses, identifying recombination patterns.
- Confirmed RAT's applicability to various sequence lengths, from viral segments to whole genomes.
Conclusions:
- RAT is a valuable and accessible tool for studying genome evolution through recombination analysis.
- The tool's intuitive design and flexibility make it suitable for diverse research applications in bioinformatics.
- RAT facilitates detailed investigation of viral evolution, as exemplified by its application to HIV and Norovirus sequences.