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RAT / Recombination Analysis Tool
Helps in finding viral recombinants. RAT is a cross-platform, Java-based application intended for high-throughput, recombination analysis of both DNA and protein multiple sequence alignments, in any one of seven different file formats. It uses the distance-based method of recombination detection. This application indicates large-scale recombination occurs in the Noroviruses. Users can employ this method to examine sequences individually using the Single-sequence viewer, or use the Auto Search option that searches for recombination given a user-defined search criterion.
Identifies DNA recombination spots. iRSpot-EL is formed by fusing various modes of pseudo nucleotide components as well as dinucleotide-based auto-cross covariance into an ensemble classifier. The new predictor not only allows users to select their desired parameters but is also more natural in conducting the genome-wide analysis due to its built-in flexible sliding window approach. Particularly, compared with the existing predictors in this area, iRSpot-EL is more accurately and stable.
Identifies the recombination hotspots and coldspots with trinucleotide composition and pseudo amino acid components. iRSpot-TNCPseAAC is an online predictor in which a DNA sample was formulated by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample according to its genetic codes. It can be use as a useful tool for identifying the recombination spots in DNA, or at the very least a complementary tool to iRSpot-PseDNC.
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