Detail výsledku

A dynamic programming algorithm for identification of triplex-forming sequences

LEXA, M.; MARTÍNEK, T.; BURGETOVÁ, I.; KOPEČEK, D.; BRÁZDOVÁ, M. A dynamic programming algorithm for identification of triplex-forming sequences. BIOINFORMATICS, 2011, vol. 27, no. 18, p. 2510-2517. ISSN: 1367-4803.
Typ
článek v časopise
Jazyk
anglicky
Autoři
Lexa Matej, Ing., Ph.D., UPSY (FIT)
Martínek Tomáš, doc. Ing., Ph.D., UPSY (FIT)
Burgetová Ivana, Ing., Ph.D., UIFS (FIT)
Kopeček Daniel
Brázdová Marie
Abstrakt

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.

Klíčová slova

DNA sequence analysis; H-DNA; triplex; triplet; triad; gene regulation; pattern search; pattern recognition

Rok
2011
Strany
2510–2517
Časopis
BIOINFORMATICS, roč. 27, č. 18, ISSN 1367-4803
DOI
10.1093/bioinformatics/btr439
UT WoS
000294755400006
EID Scopus
2-s2.0-80052776231
BibTeX 
@article{BUT76462,
  author="Matej {Lexa} and Tomáš {Martínek} and Ivana {Burgetová} and Daniel {Kopeček} and Marie {Brázdová}",
  title="A dynamic programming algorithm for identification of triplex-forming sequences",
  journal="BIOINFORMATICS",
  year="2011",
  volume="27",
  number="18",
  pages="2510--2517",
  doi="10.1093/bioinformatics/btr439",
  issn="1367-4803"
}
Projekty
Bioinformatická a experimentální identifikace nekanonických struktur v geonomové DNA, GAČR, Standardní projekty, GA204/08/1560, zahájení: 2008-04-01, ukončení: 2010-12-31, ukončen
Pokročilé bezpečné, spolehlivé a adaptivní IT, VUT, Vnitřní projekty VUT, FIT-S-11-1, zahájení: 2011-01-01, ukončení: 2013-12-31, ukončen
Výzkum informačních technologií z hlediska bezpečnosti, MŠMT, Institucionální prostředky SR ČR (např. VZ, VC), MSM0021630528, zahájení: 2007-01-01, ukončení: 2013-12-31, řešení
Výzkumné skupiny
Výzkumná skupina reprogramovatelných architektur (VZ FPGA)
Pracoviště
Ústav počítačových systémů (UPSY)
Nahoru