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iNuc-PhysChem

swMATH ID: 22453
Software Authors: Chen, W.; Lin, H.; Feng, P. M.; Ding, C.; Zuo, Y. C.; Chou, K. C.
Description: iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties. Nucleosome positioning has important roles in key cellular processes. Although intensive efforts have been made in this area, the rules defining nucleosome positioning is still elusive and debated. In this study, we carried out a systematic comparison among the profiles of twelve DNA physicochemical features between the nucleosomal and linker sequences in the Saccharomyces cerevisiae genome. We found that nucleosomal sequences have some position-specific physicochemical features, which can be used for in-depth studying nucleosomes. Meanwhile, a new predictor, called iNuc-PhysChem, was developed for identification of nucleosomal sequences by incorporating these physicochemical properties into a 1788-D (dimensional) feature vector, which was further reduced to a 884-D vector via the IFS (incremental feature selection) procedure to optimize the feature set. It was observed by a cross-validation test on a benchmark dataset that the overall success rate achieved by iNuc-PhysChem was over 96
Homepage: https://www.ncbi.nlm.nih.gov/pubmed/23144709
Related Software: iRSpot-PseDNC; iSNO-PseAAC; iRSpot-TNCPseAAC; propy; Cell-PLoc; iNuc-PseKNC; PseKNC; Pse-in-One; iCDI-PseFpt; iLoc-Hum; iEzy-drug; iHSP-PseRAAAC; PseAAC-Builder; iLoc-Animal; iNitro-Tyr; iRNAm5C-PseDNC; iSNO-AAPair; iLoc-Euk; iAMP-2L; iRNA-PseColl
Cited in: 24 Publications

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