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A dynamic programming algorithm for identification of triplex-forming sequences

LEXA Matej, MARTÍNEK Tomáš, BURGETOVÁ Ivana, KOPEČEK Daniel and BRÁZDOVÁ Marie. A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics, vol. 27, no. 18, pp. 2510-2517. ISSN 1367-4803.
Czech title
Algoritmus dynamického programování pro identifikaci sekvencí tvořících triplexy
journal article
Lexa Matej, Ing., Ph.D. (DCSY FIT BUT)
Martínek Tomáš, Ing., Ph.D. (DCSY FIT BUT)
Burgetová Ivana, Ing., Ph.D. (DIFS FIT BUT)
Kopeček Daniel (FI MUNI)
Brázdová Marie, Mgr., Ph.D. (IBP)
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.
Bioinformatics, vol. 27, no. 18, ISSN 1367-4803
Oxford University Press
   author = "Matej Lexa and Tom\'{a}\v{s} Mart\'{i}nek and Ivana Burgetov\'{a} and Daniel Kope\v{c}ek and Marie Br\'{a}zdov\'{a}",
   title = "A dynamic programming algorithm for identification of triplex-forming sequences",
   pages = "2510--2517",
   journal = "Bioinformatics",
   volume = 27,
   number = 18,
   year = 2011,
   ISSN = "1367-4803",
   doi = "10.1093/bioinformatics/btr439",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/9773"
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