Identification of human gene functional regions based on oligonucleotide composition

Proc Int Conf Intell Syst Mol Biol. 1993:1:371-9.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Exons / genetics
  • Genome, Human*
  • Humans
  • Introns / genetics
  • Mathematical Computing*
  • Models, Genetic
  • Models, Molecular
  • Oligonucleotides / genetics
  • Open Reading Frames / genetics*
  • RNA Splicing*
  • Sequence Analysis, DNA / methods*

Substances

  • Oligonucleotides