Prediction of Translation Initiation Sites on the Genome of Synechocystis sp. Strain PCC6803 by Hidden Markov Model

We developed a computer program, GeneHackerTL, which predictsthe most probable translation initiation site for a given nucleotidesequence. The program requires that information be extractedfrom the nucleotide sequence data surrounding the translationinitiation sites according to the framework of the Hidden MarkovModel. Since the translation initiation sites of 72 highly abundantproteins have already been assigned on the genome of Synechocystissp. strain PCC6803 by amino-terminal analysis, we extractednecessary information for GeneHackerTL from the nucleotide sequencedata. The prediction rate of the GeneHackerTL for these proteinswas estimated to be 86.1%. We then used GeneHackerTL for predictionof the translation initiation sites of 24 other proteins, ofwhich the initiation sites were not assigned experimentally,because of the lack of a potential initiation codon at the amino-terminalposition. For 20 out of the 24 proteins, the initiation siteswere predicted in the upstream of their amino-terminal positions.According to this assignment, the processed regions representa typical feature of signal peptides. We could also predictmultiple translation initiation sites for a particular genefor which at least two initiation sites were experimentallydetected. This program would be e.ective for the predictionof translation initiationsites of other proteins, not only inthis species but also in other prokaryotes as well.