Before we begin our exploration of the various gene-finding strategies, we need to establish a set of methods for assessing and comparing the predictive accuracy of gene finders. The two main issues that must be addressed are: (1) the experimental protocol for obtaining a set of predictions for evaluation, including the collection, filtering, and preprocessing of a suitable set of test genes, and (2) the actual evaluation metrics and their computation. The importance of obtaining an objective assessment of gene finder accuracy should not be underestimated; the publication of flawed evaluations and comparative studies can effect a significant disservice to the field by reducing interest in what might otherwise be fruitful areas of inquiry or by fostering the additional expenditure of resources on methods having no real merit. For this reason, we consider this topic to be as important as that of the actual prediction methods employed.

Testing protocols

Although computational gene predictions can be utilized in a number of different ways by manual and automatic genome annotation efforts, it is arguably the case that the application of greatest practical significance for ab initio gene finders is the detection of functional genes which have not yet been discovered through other means. An obvious implication of this is that the greatest value of a gene finder comes from its ability to recognize even those genes that were not presented as examples to the gene finder during training.