title: A dynamic programming algorithm for identification of triplex-forming sequences.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  lexa@fi.muni.cz
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Information Technology, Faculty of Informatics, Masaryk University, 60200 Brno, Czech Republic. lexa@fi.muni.cz
authors.forename: Matej
authors.initials: M
authors.lastname: Lexa
authors.forename: Tomáš
authors.initials: T
authors.lastname: Martínek
authors.forename: Ivana
authors.initials: I
authors.lastname: Burgetová
authors.forename: Daniel
authors.initials: D
authors.lastname: Kopeček
authors.forename: Marie
authors.initials: M
authors.lastname: Brázdová
mesh_terms: D000465:Algorithms; D020137:Base Pair Mismatch; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D048168:Escherichia coli K12 / Q000235:genetics*; D016678:Genome; D006801:Humans; D055029:Inverted Repeat Sequences; D016013:Likelihood Functions; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: C051802:triplex DNA; D004247:DNA