Title | ||
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Identification of human gene functional regions based on oligonucleotide composition. |
Abstract | ||
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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. |
Year | Venue | Keywords |
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1993 | ISMB | human gene functional,oligonucleotide composition,gene structure,artificial neural network,genomic dna |
Field | DocType | Volume |
Gene,Biology,splice,Exon,Coding region,RNA splicing,Intron,Bioinformatics,Genetics,GenBank,genomic DNA | Conference | 1 |
ISSN | ISBN | Citations |
1553-0833 | 0-929280-47-4 | 5 |
PageRank | References | Authors |
2.81 | 3 | 2 |
Name | Order | Citations | PageRank |
---|---|---|---|
Victor V. Solovyev | 1 | 193 | 35.93 |
C. B. Lawrence | 2 | 22 | 9.04 |