A dynamic programming algorithm for identification of triplex-forming sequences

Motivation: 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 triple...

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Published in:Bioinformatics Vol. 27; no. 18; pp. 2510 - 2517
Main Authors: Lexa, Matej, Martínek, Tomáš, Burgetová, Ivana, Kopeček, Daniel, Brázdová, Marie
Format: Journal Article
Language:English
Published: Oxford Oxford University Press 15.09.2011
Subjects:
Algorithms
Base Pair Mismatch
Base Sequence
Biological and medical sciences
DNA - chemistry
DNA - metabolism
Escherichia coli K12 - genetics
Fundamental and applied biological sciences. Psychology
General aspects
Genome
Humans
Inverted Repeat Sequences
Likelihood Functions
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Nucleic Acid Conformation
Sequence Analysis, DNA - methods
System identification
Dynamic programming
Dynamics
Algorithm
ISSN:1367-4803, 1367-4811, 1367-4811, 1460-2059
Online Access:Get full text
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Summary:Motivation: 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. Results: 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. Availability: Our implementation of the algorithm is available at http://www.fi.muni.cz/lexa/triplex as source code and a web-based search tool. The source code compiles into a library providing searching capability to other programs, as well as into a stand-alone command-line application based on this library. Contact:  lexa@fi.muni.cz Supplementary Information:  Supplementary data are available at Bioinformatics online.
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ISSN:1367-4803
1367-4811
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btr439