Optimization of Coding Potentials Using Positional Dependence of Nucleotide Frequencies

Optimization of Coding Potentials Using Positional Dependence of Nucleotide Frequencies

We study the coding potential of human DNA sequences, using the positional asymmetry function (Dp) and the positional information function (Iq). Both DpandIq are based on the positional dependence of single nucleotide frequencies. We investigate the accuracy ofDp and Iqin distinguishing coding and n...

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Veröffentlicht in:Journal of theoretical biology 2000-10, Vol.206 (4), p.525-537
Hauptverfasser: HOLSTE, DIRK, GROSSE, IVO, BULDYREV, SERGEY V., EUGENE STANLEY, H., HERZEL, HANSPETER
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Codon
Genome, Human
Humans
Models, Genetic
Sequence Analysis, DNA
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container_end_page 537
container_issue 4
container_start_page 525
container_title Journal of theoretical biology
container_volume 206
creator HOLSTE, DIRK
GROSSE, IVO
BULDYREV, SERGEY V.
EUGENE STANLEY, H.
HERZEL, HANSPETER
description We study the coding potential of human DNA sequences, using the positional asymmetry function (Dp) and the positional information function (Iq). Both DpandIq are based on the positional dependence of single nucleotide frequencies. We investigate the accuracy ofDp and Iqin distinguishing coding and non-coding DNA as a function of the parametersp and q, respectively, and explore at which parameters poptand qoptbothDp and Iqdistinguish coding and non-coding DNA most accurately. We compare our findings with classically used parameter values and find that optimized coding potentials yield comparable accuracies as classical frame-independent coding potentials trained on prior data. We find that poptand qoptvary only slightly with the sequence length.
doi_str_mv 10.1006/jtbi.2000.2144
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Genome, Human
Humans
Models, Genetic
Sequence Analysis, DNA
title Optimization of Coding Potentials Using Positional Dependence of Nucleotide Frequencies
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