Detail publikace

A dynamic programming algorithm for identification of triplex-forming sequences

LEXA, M. MARTÍNEK, T. BURGETOVÁ, I. KOPEČEK, D. BRÁZDOVÁ, M.

Originální název

A dynamic programming algorithm for identification of triplex-forming sequences

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální 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

Autoři

LEXA, M.; MARTÍNEK, T.; BURGETOVÁ, I.; KOPEČEK, D.; BRÁZDOVÁ, M.

Rok RIV

2011

Vydáno

21. 9. 2011

ISSN

1367-4803

Periodikum

BIOINFORMATICS

Ročník

27

Číslo

18

Stát

Spojené království Velké Británie a Severního Irska

Strany od

2510

Strany do

2517

Strany počet

8

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"
}