The web-server iRSpot-PseDNC was developed for identifying the recombination hotspots and coldspots. See Figure 1 below for an illustration about the recombination of DNA. The current predictor is featured by formulating the DNA samples with a novel feature vector, the so-called pseudo dinucleotide composition (PseDNC), by which six local DNA structural properties, i.e., three angular parameters (twist, tilt, and roll) and three translational parameters (shift, slide, and rise), are incorporated. It was observed by the rigorous jackknife test that the overall success rate achieved by iRSpot-PseDNC was over 82% in identifying recombination spots in Saccharomyces cerevisiae.
Figure 1. A schematic drawing to show the meiotic recombination pathways in a DNA system. Recombination is initiated by a double-strand break (DSB) catalyzed by the Spo11 protein (green ball). After DSBs are formed, Spo11 is removed from the DNA molecule (blue helix) and the single-stranded 3' ends are formed. These tails undergo strand invasion of intact homologous duplexes (red helix), ultimately yielding mature recombinant products. The repair of meiotic DSB can result in either reciprocal exchange of the chromosome arms flanking the break (a crossover) as shown in the left lower panel, or no exchange of flanking arms (a noncrossover or parental configuration) as shown in the right lower panel.
(1) The input sequences must be in FASTA format; i.e., each DNA sequence should start with a greater-than symbol (" > ") in the first column. The words right after the " > " symbol in the single initial line are optional and only used for the purpose of identification and description.
(2) All the characters in a query sequence must be valid code, i.e., A, C, G, or T; otherwise, prediction will be forced to stop.