Biomedical subjects

V V Solovyev

Publications and source records attributed to V V Solovyev.

21 records · Page 2Linked to original sources

PubMed1993

A novel method of protein sequence classification based on oligopeptide frequency analysis and its application to search for functional sites and to domain localization.

A new method for distinguishing among protein families based on the analysis of oligopeptide composition of amino acid sequences is presented. It is assumed that any protein family can be characterized by a set of essential oligopeptides (oligopeptide vocabulary). A simple approach to find such a vocabulary is suggested. It is shown that comparison of the vocabularies can distinguish among different families and the latter from random sequences. This comparison can be successfully made with a small set of frequencies of 25 dipeptides (or tripeptides). No preliminary alignment is necessary. It is established that characteristic peptides are located in the regions of functional value, as shown for GTP-binding domains of the translation elongation factors. It is demonstrated that this method is reasonably efficient for localizing functional domains in the amino acid sequences. The average error of prediction does not exceed three or four amino acid residues as shown for several functional domains.

Algorithms↗

PubMed1993

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.

Exons↗

PubMed1991

New elements of glucocorticoid-receptor binding sites of hormone-regulated genes.

The structure of the DNA regions recognized by glucocorticoid-receptor complexes (GIRC) was analyzed using frequency matrices and a modified perceptron method. Some complementary conservative elements which may modulate the efficiency of GIRC binding were found at both sides of the previously established conserved nucleotide sequence (core) (Beato, M. et al. (1987) J. Steroid Biochem. 27, 9-14). A criterion based on the concurrent use of several perceptron matrices to search for the potential GIRC binding site sequences has been worked out. By applying this criterion 73 sites were identified in 28 sequences of glucocorticoid regulated genes and 7 sites were identified in 26 sequences independent from glucocorticoid regulation.

Amino Acid Sequence↗