V. V. Solovyev and C. B. Lawrence
Accurate recognition of coding and intron regions within large regions of uneharacterized genomic DNA is an unsolved problem. A data base of more than 4240791 bp coding and 7790682 bp noncoding human sequences was extracted from GenBank to develop a function for locating coding regions in anonymousequences. Several coding measures based on oligonucleotide preferences were tested on a control set that including 1/3 of all extracted sequences. An accuracy of separation of coding/noncoding regions is 87% for 9 bp oligonucleotides on 54 bp windows and 91% on 108 bp windows, respectively. For separation of coding/ intron regions the accuracy is 89-90% for 8 bp oligonucleotides on 54 bp windows and up to 95% on 108 bp windows. Using the information about preferences of octanucleotides in protein coding and intron regions and significant triplet frequencies as a function of position near splice junctions, a joint splice site prediction scheme was developed. The accuracy of the joint scheme for predicting splice site positions on the test set was about 96-97%, which exceeds the accuracy of the previously reported splice site selection method based on a more complex artificial neural network approach. A model of splicing using poly-G(C) rich exon flanking sequences is suggested. A remarkable difference of oligonucleotide composition 5- and 3- gene regions is displayed and applied in a gene structure predictive system.