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CyclinPred: a SVM-based method for predicting cyclin protein sequences.

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title CyclinPred: a SVM-based method for predicting cyclin protein sequences.
 
Creator Kalita, Mridul K
Nandal, Umesh K
Pattnaik, Ansuman
Sivalingam, Anandhan
Ramasamy, Gowthaman
Kumar, Manish
Raghava, G.P.S.
Gupta, D
 
Subject QR Microbiology
 
Description Functional annotation of protein sequences with low similarity to well characterized protein sequences is a major challenge of computational biology in the post genomic era. The cyclin protein family is once such important family of proteins which consists of sequences with low sequence similarity making discovery of novel cyclins and establishing orthologous relationships amongst the cyclins, a difficult task. The currently identified cyclin motifs and cyclin associated domains do not represent all of the identified and characterized cyclin sequences. We describe a Support Vector Machine (SVM) based classifier, CyclinPred, which can predict cyclin sequences with high efficiency. The SVM classifier was trained with features of selected cyclin and non cyclin protein sequences. The training features of the protein sequences include amino acid composition, dipeptide composition, secondary structure composition and PSI-BLAST generated Position Specific Scoring Matrix (PSSM) profiles. Results obtained from Leave-One-Out cross validation or jackknife test, self consistency and holdout tests prove that the SVM classifier trained with features of PSSM profile was more accurate than the classifiers based on either of the other features alone or hybrids of these features. A cyclin prediction server--CyclinPred has been setup based on SVM model trained with PSSM profiles. CyclinPred prediction results prove that the method may be used as a cyclin prediction tool, complementing conventional cyclin prediction methods.
 
Publisher PLoS
 
Date 2008
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://crdd.osdd.net/open/38/1/raghava2008.3.pdf
Kalita, Mridul K and Nandal, Umesh K and Pattnaik, Ansuman and Sivalingam, Anandhan and Ramasamy, Gowthaman and Kumar, Manish and Raghava, G.P.S. and Gupta, D (2008) CyclinPred: a SVM-based method for predicting cyclin protein sequences. PloS one, 3 (7). e2605. ISSN 1932-6203
 
Relation http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002605
http://crdd.osdd.net/open/38/