Publication result detail

A dynamic programming algorithm for identification of triplex-forming sequences

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

Original Title

A dynamic programming algorithm for identification of triplex-forming sequences

English Title

A dynamic programming algorithm for identification of triplex-forming sequences

Type

WoS Article

Original 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.

English 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

Key words in English

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

Authors

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

RIV year

2012

Released

21.09.2011

ISBN

1367-4803

Periodical

BIOINFORMATICS

Volume

27

Number

18

State

United Kingdom of Great Britain and Northern Ireland

Pages from

2510

Pages to

2517

Pages count

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"
}