title: Subsequence-based feature map for protein function classification.
abstract: Automated classification of proteins is indispensable for further in vivo investigation of excessive number of unknown sequences generated by large scale molecular biology techniques. This study describes a discriminative system based on feature space mapping, called subsequence profile map (SPMap) for functional classification of protein sequences. SPMap takes into account the information coming from the subsequences of a protein. A group of protein sequences that belong to the same level of classification is decomposed into fixed-length subsequences and they are clustered to obtain a representative feature space mapping. Mapping is defined as the distribution of the subsequences of a protein sequence over these clusters. The resulting feature space representation is used to train discriminative classifiers for functional families. The aim of this approach is to incorporate information coming from important subregions that are conserved over a family of proteins while avoiding the difficult task of explicit motif identification. The performance of the method was assessed through tests on various protein classification tasks. Our results showed that SPMap is capable of high accuracy classification in most of these tasks. Furthermore SPMap is fast and scalable enough to handle large datasets.
authors.affiliation: Department of Computer Engineering, Middle East Technical University, 06531 Ankara, Turkey.
authors.forename: Omer Sinan
authors.initials: OS
authors.lastname: Sarac
authors.forename: Ozge
authors.initials: O
authors.lastname: Gürsoy-Yüzügüllü
authors.forename: Rengul
authors.initials: R
authors.lastname: Cetin-Atalay
authors.forename: Volkan
authors.initials: V
authors.lastname: Atalay
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry / Q000145:classification; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000145:classification*; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry / Q000145:classification; D012680:Sensitivity and Specificity
chemical_list: D004798:Enzymes; D011506:Proteins; D043562:Receptors, G-Protein-Coupled