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

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 m...

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Autores principales:	Mridul K Kalita, Umesh K Nandal, Ansuman Pattnaik, Anandhan Sivalingam, Gowthaman Ramasamy, Manish Kumar, Gajendra P S Raghava, Dinesh Gupta
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5a09ed92bf1f43c0a1fccdb63e09f612
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id	oai:doaj.org-article:5a09ed92bf1f43c0a1fccdb63e09f612
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spelling	oai:doaj.org-article:5a09ed92bf1f43c0a1fccdb63e09f6122021-11-25T06:11:50ZCyclinPred: a SVM-based method for predicting cyclin protein sequences.1932-620310.1371/journal.pone.0002605https://doaj.org/article/5a09ed92bf1f43c0a1fccdb63e09f6122008-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18596929/?tool=EBIhttps://doaj.org/toc/1932-6203Functional 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.Mridul K KalitaUmesh K NandalAnsuman PattnaikAnandhan SivalingamGowthaman RamasamyManish KumarGajendra P S RaghavaDinesh GuptaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 7, p e2605 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mridul K Kalita Umesh K Nandal Ansuman Pattnaik Anandhan Sivalingam Gowthaman Ramasamy Manish Kumar Gajendra P S Raghava Dinesh Gupta CyclinPred: a SVM-based method for predicting cyclin protein sequences.
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.
format	article
author	Mridul K Kalita Umesh K Nandal Ansuman Pattnaik Anandhan Sivalingam Gowthaman Ramasamy Manish Kumar Gajendra P S Raghava Dinesh Gupta
author_facet	Mridul K Kalita Umesh K Nandal Ansuman Pattnaik Anandhan Sivalingam Gowthaman Ramasamy Manish Kumar Gajendra P S Raghava Dinesh Gupta
author_sort	Mridul K Kalita
title	CyclinPred: a SVM-based method for predicting cyclin protein sequences.
title_short	CyclinPred: a SVM-based method for predicting cyclin protein sequences.
title_full	CyclinPred: a SVM-based method for predicting cyclin protein sequences.
title_fullStr	CyclinPred: a SVM-based method for predicting cyclin protein sequences.
title_full_unstemmed	CyclinPred: a SVM-based method for predicting cyclin protein sequences.
title_sort	cyclinpred: a svm-based method for predicting cyclin protein sequences.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/5a09ed92bf1f43c0a1fccdb63e09f612
work_keys_str_mv	AT mridulkkalita cyclinpredasvmbasedmethodforpredictingcyclinproteinsequences AT umeshknandal cyclinpredasvmbasedmethodforpredictingcyclinproteinsequences AT ansumanpattnaik cyclinpredasvmbasedmethodforpredictingcyclinproteinsequences AT anandhansivalingam cyclinpredasvmbasedmethodforpredictingcyclinproteinsequences AT gowthamanramasamy cyclinpredasvmbasedmethodforpredictingcyclinproteinsequences AT manishkumar cyclinpredasvmbasedmethodforpredictingcyclinproteinsequences AT gajendrapsraghava cyclinpredasvmbasedmethodforpredictingcyclinproteinsequences AT dineshgupta cyclinpredasvmbasedmethodforpredictingcyclinproteinsequences
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CyclinPred: a SVM-based method for predicting cyclin protein sequences.

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