Publication Details
A dynamic programming algorithm for identification of triplex-forming sequences
Martínek Tomáš, doc. Ing., Ph.D. (DCSY)
Burgetová Ivana, Ing., Ph.D. (DIFS)
Kopeček Daniel
Brázdová Marie
DNA sequence analysis; H-DNA; triplex; triplet; triad; gene regulation; pattern search; pattern recognition
Current methods for identification of potential triplex-forming sequences in genomes and similar sequence sets rely primarily on detecting homopurine and homopyrimidine tracts. Procedures capable of detecting sequences supporting imperfect, but structurally feasible intramolecular triplex structures are needed for better sequence analysis. 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.
@article{BUT76462,
author="Matej {Lexa} and Tomáš {Martínek} and Ivana {Burgetová} and Daniel {Kopeček} and Marie {Brázdová}",
title="A dynamic programming algorithm for identification of triplex-forming sequences",
journal="BIOINFORMATICS",
year="2011",
volume="27",
number="18",
pages="2510--2517",
doi="10.1093/bioinformatics/btr439",
issn="1367-4803"
}