Abstract

Driven by the rapid growth of the complete genome sequences, it is accepted that genome annotation has been resorted mostly to automatic methodology. For computational annotation to bacterial and archaeal genomes, accurate prediction of translation initiation sites (TISs) is essential to locate protein coding regions of genes. Therefore, TIS prediction has been a challenge to a number of gene finders and TIS processors, leading to recent studies of TIS prediction or correction in prokaryotic genome annotation as well as of the mechanism of translation initiation. It is time for the research community to review the available mathematical models of TIS of prokaryotic gene, and the resultant algorithms for a series of current TIS processors and TIS prediction modules in gene finders. In fact, the TIS models have been improved along with the knowledge of the mechanism of translation initiation. Several studies of the mechanism of translation initiation in prokaryotic genomes have been summarized. With a few of published data sets widely-used in evaluation of TIS identification, the performances of the existing methods are assessed and discussed in this article. It is also interesting to discuss the relation between the algorithms and the understanding of prokaryotic translation initiation mechanism, which can enlighten us on the state-of-the-art studies of TIS prediction in bacterial and archaeal genomes.

Keywords: Algorithms, prediction, prokaryotic genome, translation initiation sites.