GeneMark-RC, a Recursive Procedure for Gene Identi cation in the Genomic Sequence Data with Self-Consistency Evaluation; Its Application to the Analysis of Several Prokaryotic Genomes

Previously, we developed a GeneMark-based procedure, termed GeneMark-RC, and applied it for the identi cation and classi cation of ORFs in genomic sequence data, and identi ed and characterized ORFs in the 1.0 Mb data of the cyanobacterium Synechocystis sp. strain PCC 6803. In the present study, we have improved the procedure and performed analysis of the whole genomic data of Synechocystis. Consequently, we noticed the presence of three distinct classes of ORFs in this organism. The prediction of ORFs by the class-speci c GeneMark-RC analysis agreed with 97.9 % of those described for this bacterium. Moreover, 124 additional ORFs were identi ed. The procedure was similarly applied to the genomic analysis of ve other prokaryotes, and 2 to 3 classes of ORFs were recognized in each case. Common features were found among the ORFs identi ed in the six organisms including Synechocystis. Class 1 is composed of most typical ORFs whose GC content is slightly higher than the average, while Class 2 is composed of ORFs with GC contents lower than the average. It was found that ORFs of one species can be detected with the GeneMarkRC parameters obtained from other organisms, and the prediction rate is high when the di erence in their GC contents is small. It was also found that ORFs of three species with relatively low GC contents can be nicely detected with the Synechocystis matrices of Class 2 ORFs whose GC content is similar to that of the three species. Therefore, although there are two to three classes of ORFs in each species, their di-codon statistics must be rather similar to each other if their GC contents are similar. A notable exception was the case of Methanococcus jannaschii, which might re ect the fact that it is an archaebacterium.