About: A dynamic programming algorithm for identification of triplex-forming sequences

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Description	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 satisf 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 satisf (en)
Title	A dynamic programming algorithm for identification of triplex-forming sequences A dynamic programming algorithm for identification of triplex-forming sequences (en)
skos:prefLabel	A dynamic programming algorithm for identification of triplex-forming sequences A dynamic programming algorithm for identification of triplex-forming sequences (en)
skos:notation	RIV/00216305:26230/11:PU96166!RIV13-GA0-26230___
http://linked.open...avai/predkladatel	Fakulta informačních technologií
http://linked.open...avai/riv/aktivita	P S Z
http://linked.open...avai/riv/aktivity	P(GA204/08/1560), S, Z(MSM0021630528)
http://linked.open...iv/cisloPeriodika	18
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Martínek, Tomáš Burgetová, Ivana Lexa, Matej
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Vysoké učení technické v Brně / Fakulta informačních technologií
http://linked.open...dnocenehoVysledku	183775
http://linked.open...ai/riv/idVysledku	RIV/00216305:26230/11:PU96166
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	DNA sequence analysis, H-DNA, triplex, triplet, triad, gene regulation, pattern search, pattern recognition (en)
http://linked.open.../riv/klicoveSlovo	DNA sequence analysis H-DNA gene regulation pattern recognition pattern search triad triplet triplex
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[FA38C1EDFDA6]
http://linked.open...i/riv/nazevZdroje	BIOINFORMATICS
http://linked.open...in/vavai/riv/obor	IN
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	In vitro and in silico identification of non-canonical DNA structures in genomic DNA sequences
http://linked.open...UplatneniVysledku	2011
http://linked.open...v/svazekPeriodika	27
http://linked.open...iv/tvurceVysledku	Burgetová, Ivana Brázdová, Marie Kopeček, Daniel Lexa, Matej Martínek, Tomáš
http://linked.open...ain/vavai/riv/wos	000294755400006
http://linked.open...n/vavai/riv/zamer	Výzkum informačních technologií z hlediska bezpečnosti
issn	1367-4803
number of pages	8 (xsd:int)
http://bibframe.org/vocab/doi	10.1093/bioinformatics/btr439
http://localhost/t...ganizacniJednotka	26230
is http://linked.open...avai/riv/vysledek of	A dynamic programming algorithm for identification of triplex-forming sequences

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