Identification of human gene functional regions based on oligonucleotide composition.
Accurate recognition of coding and intron regions within large regions of uncharacterized genomic DNA is an unsolved problem. A data base of more than 4,240,791 bp coding and 7,790,682 bp noncoding human sequences was extracted from GenBank to develop a function for locating coding regions in anonymous sequences. 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.
Solovyev
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VV
Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA.
Lawrence
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CB
D005091:Exons / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D007438:Introns / Q000235:genetics; D008432:Mathematical Computing; D008957:Models, Genetic; D008958:Models, Molecular; D009841:Oligonucleotides / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D012326:RNA Splicing; D017422:Sequence Analysis, DNA / Q000379:methods*
D009841:Oligonucleotides