Hybrid biogeography based simultaneous feature selection and MHC class I peptide binding prediction using support vector machines and random forests.
Accurate detection of peptides binding to specific Major Histocompatibility Complex Class I (MHC-I) molecules is extremely important for understanding the underlying process of the immune system, as well as for effective vaccine design and developing immunotherapies. Development of learning algorithms and their application for binding predictions have thus speeded up the state-of-the-art in immunological research, in a cost-effective manner. In this work, we propose the application of a hybrid filter-wrapper algorithm employing concepts from the recently developed biogeography based optimization algorithm, in conjunction with SVM and Random Forests for identification of MHC-I binding peptides. In the process, we demonstrate the effectiveness of this evolutionary technique, coupled with weighted heuristics, for the construction of improved prediction models. The experiments have been carried out for the CoEPrA competition datasets (accessible online at: http://www.coepra.org) and the results show a marked improvement over the winner results in some situations and comparably good with regard to others .We thus hope to initiate further research on the application of this new bio-inspired methodology for immunological research.
Dr DY Patil Biotechnology and Bioinformatics Institute, Padmashree Dr DY Patil University, Pune, Maharashtra, India. atuljisrivastava@gmail.com
Atulji
A
Srivastava
Shameek
S
Ghosh
N
N
Anantharaman
V K
VK
Jayaraman
D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D015395:Histocompatibility Antigens Class I / Q000276:immunology / Q000378:metabolism*; D009842:Oligopeptides / Q000145:classification / Q000276:immunology / Q000378:metabolism*; D011485:Protein Binding / Q000276:immunology; D012044:Regression Analysis; D015203:Reproducibility of Results; D060388:Support Vector Machine
D015395:Histocompatibility Antigens Class I; C408902:MHC binding peptide; D009842:Oligopeptides