| LEXA, Matej, Tomáš MARTÍNEK, Ivana BURGETOVÁ, Daniel KOPEČEK and Marie BRÁZDOVÁ. A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics. Oxford: Oxford University Press, 2011, vol. 27, No 18, p. 2510-2517. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btr439. |
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@article{947322,
author = {Lexa, Matej and Martínek, Tomáš and Burgetová, Ivana and Kopeček, Daniel and Brázdová, Marie},
article_location = {Oxford},
article_number = {18},
doi = {http://dx.doi.org/10.1093/bioinformatics/btr439},
keywords = {DNA sequence analysis; H-DNA; triplex; triplet; triad; gene regulation; pattern search; pattern recognition},
language = {eng},
issn = {1367-4803},
journal = {Bioinformatics},
title = {A dynamic programming algorithm for identification of triplex-forming sequences},
url = {http://bioinformatics.oxfordjournals.org/content/early/2011/07/26/bioinformatics.btr439.abstract},
volume = {27},
year = {2011}
}
TY - JOUR
ID - 947322
AU - Lexa, Matej - Martínek, Tomáš - Burgetová, Ivana - Kopeček, Daniel - Brázdová, Marie
PY - 2011
TI - A dynamic programming algorithm for identification of triplex-forming sequences
JF - Bioinformatics
VL - 27
IS - 18
SP - 2510-2517
EP - 2510-2517
PB - Oxford University Press
SN - 13674803
KW - DNA sequence analysis
KW - H-DNA
KW - triplex
KW - triplet
KW - triad
KW - gene regulation
KW - pattern search
KW - pattern recognition
UR - http://bioinformatics.oxfordjournals.org/content/early/2011/07/26/bioinformatics.btr439.abstract
N2 - Current methods for identification of potential triplex-forming sequences in genomes and similar sequence sets rely primarily on detecting homopurine and homopyrimidine tracts. We modified an algorithm for detection of approximate palindromes, so as to account for the special nature of triplex DNA structures. From available literature we conclude that approximate triplexes tolerate two classes of errors. One, analogical to mismatches in duplex DNA, involves nucleotides in triplets that do not readily form Hoogsteen bonds. The other class involves geometrically incompatible neighboring triplets hindering proper alignment of strands for optimal hydrogen bonding and stacking. We tested the statistical properties of the algorithm, as well as its correctness when confronted with known triplex sequences. The proposed algorithm satisfactorily detects sequences with intramolecular triplex-forming potential. Its complexity is directly comparable to palindrome searching.
ER -
LEXA, Matej, Tomáš MARTÍNEK, Ivana BURGETOVÁ, Daniel KOPEČEK and Marie BRÁZDOVÁ. A dynamic programming algorithm for identification of triplex-forming sequences. \textit{Bioinformatics}. Oxford: Oxford University Press, 2011, vol.~27, No~18, p.~2510-2517. ISSN~1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btr439.
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