A dynamic programming algorithm for identification of triplex-forming sequences
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26230%2F11%3APU96166" target="_blank" >RIV/00216305:26230/11:PU96166 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14330/11:00049911
Result on the web
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DOI - Digital Object Identifier
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Alternative languages
Result language
angličtina
Original language name
A dynamic programming algorithm for identification of triplex-forming sequences
Original language 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 sa
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
IN - Informatics
OECD FORD branch
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Result continuities
Project
<a href="/en/project/GA204%2F08%2F1560" target="_blank" >GA204/08/1560: In vitro and in silico identification of non-canonical DNA structures in genomic DNA sequences</a><br>
Continuities
Z - Vyzkumny zamer (s odkazem do CEZ)<br>S - Specificky vyzkum na vysokych skolach
Others
Publication year
2011
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
BIOINFORMATICS
ISSN
1367-4803
e-ISSN
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Volume of the periodical
27
Issue of the periodical within the volume
18
Country of publishing house
GB - UNITED KINGDOM
Number of pages
8
Pages from-to
2510-2517
UT code for WoS article
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EID of the result in the Scopus database
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