A dynamic programming algorithm for identification of
triplex-forming sequences

J 2011

A dynamic programming algorithm for identification of triplex-forming sequences

LEXA, Matej, Tomáš MARTÍNEK, Ivana BURGETOVÁ, Daniel KOPEČEK, Marie BRÁZDOVÁ et. al.

Základní údaje

Originální název

A dynamic programming algorithm for identification of triplex-forming sequences

Název česky

Algoritmus dynamického programování pro identifikaci sekvencí tvořících triplexy

Autoři

LEXA, Matej (703 Slovensko, garant, domácí), Tomáš MARTÍNEK (203 Česká republika), Ivana BURGETOVÁ (203 Česká republika), Daniel KOPEČEK (203 Česká republika, domácí) a Marie BRÁZDOVÁ (203 Česká republika)

Vydání

Bioinformatics, Oxford, Oxford University Press, 2011, 1367-4803

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.468

Kód RIV

RIV/00216224:14330/11:00049911

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1093/bioinformatics/btr439

UT WoS

000294755400006

Klíčová slova anglicky

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

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 20. 4. 2012 11:42, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

Current methods for identification of potential triplex-forming sequences in genomes and similar sequence sets rely primarily on detecting homopurine and homopyrimidine tracts. 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.

Návaznosti

GA204/08/1560, projekt VaV

Název: Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA

Investor: Grantová agentura ČR, Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA

Citovat

LEXA, Matej, Tomáš MARTÍNEK, Ivana BURGETOVÁ, Daniel KOPEČEK a Marie BRÁZDOVÁ. A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics. Oxford: Oxford University Press, 2011, roč. 27, č. 18, s. 2510-2517. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btr439.

@article{947322,
   author = {Lexa, Matej and Martínek, Tomáš and Burgetová, Ivana and Kopeček, Daniel and Brázdová, Marie},
   article_location = {Oxford},
   article_number = {18},
   doi = {http://dx.doi.org/10.1093/bioinformatics/btr439},
   keywords = {DNA sequence analysis; H-DNA; triplex; triplet; triad; gene regulation; pattern search; pattern recognition},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {A dynamic programming algorithm for identification of triplex-forming sequences},
   url = {http://bioinformatics.oxfordjournals.org/content/early/2011/07/26/bioinformatics.btr439.abstract},
   volume = {27},
   year = {2011}
}

TY  - JOUR
ID  - 947322
AU  - Lexa, Matej - Martínek, Tomáš - Burgetová, Ivana - Kopeček, Daniel - Brázdová, Marie
PY  - 2011
TI  - A dynamic programming algorithm for identification of triplex-forming sequences
JF  - Bioinformatics
VL  - 27
IS  - 18
SP  - 2510-2517
EP  - 2510-2517
PB  - Oxford University Press
SN  - 13674803
KW  - DNA sequence analysis
KW  - H-DNA
KW  - triplex
KW  - triplet
KW  - triad
KW  - gene regulation
KW  - pattern search
KW  - pattern recognition
UR  - http://bioinformatics.oxfordjournals.org/content/early/2011/07/26/bioinformatics.btr439.abstract
N2  - Current methods for identification of potential triplex-forming sequences in genomes and similar sequence sets rely primarily on detecting homopurine and homopyrimidine tracts. 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.
ER  -

LEXA, Matej, Tomáš MARTÍNEK, Ivana BURGETOVÁ, Daniel KOPEČEK a Marie BRÁZDOVÁ. A dynamic programming algorithm for identification of triplex-forming sequences. \textit{Bioinformatics}. Oxford: Oxford University Press, 2011, roč.~27, č.~18, s.~2510-2517. ISSN~1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btr439.

Podrobný výpis o publikaci