title: CyclinPred: a SVM-based method for predicting cyclin protein sequences.
abstract: 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.
authors.affiliation: Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Mridul K
authors.initials: MK
authors.lastname: Kalita
authors.forename: Umesh K
authors.initials: UK
authors.lastname: Nandal
authors.forename: Ansuman
authors.initials: A
authors.lastname: Pattnaik
authors.forename: Anandhan
authors.initials: A
authors.lastname: Sivalingam
authors.forename: Gowthaman
authors.initials: G
authors.lastname: Ramasamy
authors.forename: Manish
authors.initials: M
authors.lastname: Kumar
authors.forename: Gajendra P S
authors.initials: GP
authors.lastname: Raghava
authors.forename: Dinesh
authors.initials: D
authors.lastname: Gupta
mesh_terms: D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods; D016213:Cyclins / Q000737:chemistry*; D030562:Databases, Protein; D011237:Predictive Value of Tests; D025341:Principal Component Analysis; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D016213:Cyclins