title: Protein sub-nuclear localization prediction using SVM and Pfam domain information.
abstract: The nucleus is the largest and the highly organized organelle of eukaryotic cells. Within nucleus exist a number of pseudo-compartments, which are not separated by any membrane, yet each of them contains only a specific set of proteins. Understanding protein sub-nuclear localization can hence be an important step towards understanding biological functions of the nucleus. Here we have described a method, SubNucPred developed by us for predicting the sub-nuclear localization of proteins. This method predicts protein localization for 10 different sub-nuclear locations sequentially by combining presence or absence of unique Pfam domain and amino acid composition based SVM model. The prediction accuracy during leave-one-out cross-validation for centromeric proteins was 85.05%, for chromosomal proteins 76.85%, for nuclear speckle proteins 81.27%, for nucleolar proteins 81.79%, for nuclear envelope proteins 79.37%, for nuclear matrix proteins 77.78%, for nucleoplasm proteins 76.98%, for nuclear pore complex proteins 88.89%, for PML body proteins 75.40% and for telomeric proteins it was 83.33%. Comparison with other reported methods showed that SubNucPred performs better than existing methods. A web-server for predicting protein sub-nuclear localization named SubNucPred has been established at http://14.139.227.92/mkumar/subnucpred/. Standalone version of SubNucPred can also be downloaded from the web-server.
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi, India.
authors.forename: Ravindra
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi, India.
authors.forename: Sohni
authors.initials: S
authors.lastname: Jain
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi, India.
authors.forename: Bandana
authors.initials: B
authors.lastname: Kumari
authors.affiliation: Department of Biophysics, University of Delhi South Campus, New Delhi, India.
authors.forename: Manish
authors.initials: M
authors.lastname: Kumar
mesh_terms: D000465:Algorithms; D002467:Cell Nucleus / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D009687:Nuclear Proteins / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D060388:Support Vector Machine
chemical_list: D009687:Nuclear Proteins