Logic classification and feature selection for biomedical data
Computers & Mathematics with Applications
Peptide programs: applying fragment programs to protein classification
Proceedings of the 2nd international workshop on Data and text mining in bioinformatics
Protein data condensation for effective quaternary structure classification
IDEAL'07 Proceedings of the 8th international conference on Intelligent data engineering and automated learning
| Hi-index | 3.84 |
Motivation: A key goal of genomics is to assign function to genes, especially for orphan sequences. Results: We compared the clustered functional domains in the SBASE database to each protein sequence using BLASTP. This representation for a protein is a vector, where each of the non-zero entries in the vector indicates a significant match between the sequence of interest and the SBASE domain. The machine learning methods nearest neighbour algorithm (NNA) and support vector machines are used for predicting protein functional classes from this information. We find that the best results are found using the SBASE-A database and the NNA, namely 72% accuracy for 79% coverage. We tested an assigning function based on searching for InterPro sequence motifs and by taking the most significant BLAST match within the dataset. We applied the functional domain composition method to predict the functional class of 2018 currently unclassified yeast open reading frames. Availability: A program for the prediction method, that uses NNA called Functional Class Prediction based on Functional Domains (FCPFD) is available and can be obtained by contacting Y.D.Cai at y.cai@umist.ac.uk