swMATH ID: 22437
Software Authors: Chen, W.; Feng, P. -M.; Lin, H.; Chou, K. -C.
Description: iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition. Meiotic recombination is an important biological process. As a main driving force of evolution, recombination provides natural new combinations of genetic variations. Rather than randomly occurring across a genome, meiotic recombination takes place in some genomic regions (the so-called ’hotspots’) with higher frequencies, and in the other regions (the so-called ’coldspots’) with lower frequencies. Therefore, the information of the hotspots and coldspots would provide useful insights for in-depth studying of the mechanism of recombination and the genome evolution process as well. So far, the recombination regions have been mainly determined by experiments, which are both expensive and time-consuming. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the recombination regions. In this study, a predictor, called ’iRSpot-PseDNC’, was developed for identifying the recombination hotspots and coldspots. In the new predictor, the samples of DNA sequences are formulated by a novel feature vector, the so-called ’pseudo dinucleotide composition’ (PseDNC), into 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 >82
Homepage: https://www.ncbi.nlm.nih.gov/pubmed/23303794
Related Software: iSNO-PseAAC; Pse-in-One; PseKNC; iNuc-PseKNC; iRSpot-TNCPseAAC; propy; iPro54-PseKNC; LIBSVM; iLoc-Hum; iSNO-AAPair; iRNA-PseColl; pSuc-Lys; iPPI-Esml; iPTM-mLys; PseAAC-Builder; iNuc-PhysChem; pLoc-mAnimal; iRNA-AI; iRSpot-EL; 2L-piRNA
Cited in: 65 Publications
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