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. doi:10.1093/bioinformatics/btr439.
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Basic information
Original name A dynamic programming algorithm for identification of triplex-forming sequences
Name in Czech Algoritmus dynamického programování pro identifikaci sekvencí tvořících triplexy
Authors LEXA, Matej (703 Slovakia, guarantor, belonging to the institution), Tomáš MARTÍNEK (203 Czechia), Ivana BURGETOVÁ (203 Czechia), Daniel KOPEČEK (203 Czechia, belonging to the institution) and Marie BRÁZDOVÁ (203 Czechia).
Edition Bioinformatics, Oxford, Oxford University Press, 2011, 1367-4803.
Other information
Original language English
Type of outcome article in a journal
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 5.468
RIV identification code RIV/00216224:14330/11:00049911
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1093/bioinformatics/btr439
UT WoS 000294755400006
Keywords in English DNA sequence analysis; H-DNA; triplex; triplet; triad; gene regulation; pattern search; pattern recognition
Tags International impact, Reviewed
Changed by Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 20/4/2012 11:42.
Abstract
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.
Links
GA204/08/1560, research and development projectName: Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA
Investor: Czech Science Foundation, Standard Projects
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