A brief review of computational gene prediction methods

Abstract

With the development of genome sequencing for many organisms, more and more raw sequences need to be annotated. Gene prediction by computational methods for finding the location of protein coding regions is one of the essential issues in bioinformatics. Two classes of methods are generally adopted: similarity based searches and ab initio prediction. Here, we review the development of gene prediction methods, summarize the measures for evaluating predictor quality, highlight open problems in this area, and discuss future research directions.

Fig. 1

State transition of HMM modeling eukaryotic genes.

Fig. 2

Evaluation of gene prediction accuracy at the exon level.