Result Details

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.
Type
journal article
Language
English
Authors
Lexa Matej, Ing., Ph.D., DCSY (FIT)
Martínek Tomáš, doc. Ing., Ph.D., DCSY (FIT)
Burgetová Ivana, Ing., Ph.D., DIFS (FIT)
Kopeček Daniel
Brázdová Marie
Abstract

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.

Keywords

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

Published
2011
Pages
2510–2517
Journal
BIOINFORMATICS, vol. 27, no. 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"
}
Projects
Advanced secured, reliable and adaptive IT, BUT, Vnitřní projekty VUT, FIT-S-11-1, start: 2011-01-01, end: 2013-12-31, completed
In vitro and in silico identification of non-canonical DNA structures in genomic sequences, GACR, Standardní projekty, GA204/08/1560, start: 2008-04-01, end: 2010-12-31, completed
Security-Oriented Research in Information Technology, MŠMT, Institucionální prostředky SR ČR (např. VZ, VC), MSM0021630528, start: 2007-01-01, end: 2013-12-31, running
Research groups
Reconfigurable Architecture Research Group (VZ FPGA)
Departments
Department of Computer Systems (DCSY)
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