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.

Basic information

Original name

A dynamic programming algorithm for identification of triplex-forming sequences

Name in Czech

Algoritmus dynamického programování pro identifikaci sekvencí tvořících triplexy

Authors

LEXA, Matej (703 Slovakia, guarantor, belonging to the institution); Tomáš MARTÍNEK (203 Czech Republic); Ivana BURGETOVÁ (203 Czech Republic); Daniel KOPEČEK (203 Czech Republic, belonging to the institution) and Marie BRÁZDOVÁ (203 Czech Republic)

Edition

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

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 5.468

RIV identification code

RIV/00216224:14330/11:00049911

Organization unit

Faculty of Informatics

DOI

https://doi.org/10.1093/bioinformatics/btr439

UT WoS

000294755400006

Keywords in English

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

Abstract

In the original language

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.

Links

GA204/08/1560, research and development project

Name: Bioinformatická a experimentální identifikace nekanonických struktur v genomové DNA

Investor: Czech Science Foundation, In vitro and in silico identification of non-canonical DNA structures in genomic sequences

Cite

LEXA, Matej; Tomáš MARTÍNEK; Ivana BURGETOVÁ; Daniel KOPEČEK and Marie BRÁZDOVÁ. A dynamic programming algorithm for identification of triplex-forming sequences. Bioinformatics. Oxford: Oxford University Press, 2011, vol. 27, No 18, p. 2510-2517. ISSN 1367-4803. Available from: https://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 = {https://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 and Marie BRÁZDOVÁ. A dynamic programming algorithm for identification of triplex-forming sequences. \textit{Bioinformatics}. Oxford: Oxford University Press, 2011, vol.~27, No~18, p.~2510-2517. ISSN~1367-4803. Available from: https://doi.org/10.1093/bioinformatics/btr439.

Přehled o publikaci