Publication details

A dynamic programming algorithm for identification of triplex-forming sequences

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Authors

LEXA Matej MARTÍNEK Tomáš BURGETOVÁ Ivana KOPEČEK Daniel BRÁZDOVÁ Marie

Year of publication 2011
Type Article in Periodical
Magazine / Source Bioinformatics
MU Faculty or unit

Faculty of Informatics

Citation
Web http://bioinformatics.oxfordjournals.org/content/early/2011/07/26/bioinformatics.btr439.abstract
Doi http://dx.doi.org/10.1093/bioinformatics/btr439
Field Informatics
Keywords DNA sequence analysis; H-DNA; triplex; triplet; triad; gene regulation; pattern search; pattern recognition
Description 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.
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