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.
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