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Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides.

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides.
 
Creator Panwar, Bharat
Raghava, G.P.S.
 
Subject QR Microbiology
 
Description The RNA-protein interactions play a diverse role in the cells, thus identification of RNA-protein interface is essential for the biologist to understand their function. In the past, several methods have been developed for predicting RNA interacting residues in proteins, but limited efforts have been made for the identification of protein-interacting nucleotides in RNAs. In order to discriminate protein-interacting and non-interacting nucleotides, we used various classifiers (NaiveBayes, NaiveBayesMultinomial, BayesNet, ComplementNaiveBayes, MultilayerPerceptron, J48, SMO, RandomForest, SMO and SVM(light)) for prediction model development using various features and achieved highest 83.92% sensitivity, 84.82 specificity, 84.62% accuracy and 0.62 Matthew's correlation coefficient by SVM(light) based models. We observed that certain tri-nucleotides like ACA, ACC, AGA, CAC, CCA, GAG, UGA, and UUU preferred in protein-interaction. All the models have been developed using a non-redundant dataset and are evaluated using five-fold cross validation technique. A web-server called RNApin has been developed for the scientific community (http://crdd.osdd.net/raghava/rnapin/).
 
Publisher Elsevier
 
Date 2015-04
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://crdd.osdd.net/open/1665/1/GPSR%202015%20Genomics%20panwar2015.pdf
Panwar, Bharat and Raghava, G.P.S. (2015) Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides. Genomics, 105 (4). pp. 197-203. ISSN 1089-8646
 
Relation http://www.sciencedirect.com/science/article/pii/S0888754315000221
http://crdd.osdd.net/open/1665/