Ab initio gene prediction for protein-coding regions

MOTIVATION: Ab initio gene prediction in nonmodel organisms is a difficult task. While many ab initio methods have been developed, their average accuracy over long segments of a genome, and especially when assessed over a wide range of species, generally yields results with sensitivity and specificity levels in the low 60% range. A common weakness of most methods is the tendency to learn patterns that are species-specific to varying degrees. The need exists for methods to extract genetic features that can distinguish coding and noncoding regions that are not sensitive to specific organism characteristics. RESULTS: A new method based on a neural network (NN) that uses a collection of sensors to create input features is presented. It is shown that accurate predictions are achieved even when trained on organisms that are significantly different phylogenetically than test organisms. A consensus prediction algorithm for a CoDing Sequence (CDS) is subsequently applied to the first nucleotide level of NN predictions that boosts accuracy through a data-driven procedure that optimizes a CDS/non-CDS threshold. An aggregate accuracy benchmark at the nucleotide level shows that this new approach performs better than existing ab initio methods, while requiring significantly less training data. AVAILABILITY AND IMPLEMENTATION: https://github.com/BioMolecularPhysicsGroup-UNCC/MachineLearning.