Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

Background: There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl. Results: The measure of prediction success is greatly affected by the level of imbalance in the training dataset. We found the balanced dataset tha...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Richard J. B. Dobson, Patricia B. Munroe, Mark J. Caulfield, Mansoor A. S. Saqi
• Keywords: BMCBI 2006, Machine Learning Methods, Predictions, Single Nucleotide Polymorphisms