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

Anglický název

A dynamic programming algorithm for identification of triplex-forming sequences

Jazyk

en

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.

Anglický 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.

Dokumenty

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",
  annote="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.",
  address="NEUVEDEN",
  chapter="76462",
  doi="10.1093/bioinformatics/btr439",
  edition="NEUVEDEN",
  howpublished="print",
  institution="NEUVEDEN",
  number="18",
  volume="27",
  year="2011",
  month="september",
  pages="2510--2517",
  publisher="NEUVEDEN",
  type="journal article in Web of Science"
}