Supplemental materials: Lexa et al., 2011, Bioinformatics

Lexa M., Martinek T., Burgetova I., Kopecek D. and Brazdova M. (2011). Bioinformatics (doi: 10.1093/bioinformatics/btr439)

A dynamic programming algorithm for identification of triplex-forming sequences

This page provides supplementary material to the paper by Lexa et al. (2011) and a link to a web-based search tool that allows you to analyze a user-supplied DNA sequence or some of the provided genome sequence.

Errata

corrected version

Software

triplex (R/Bioconductor package for Linux/Win/Mac) We strongly encourage you to use this R/Bioconductor version. Only the R version will be maintained after April 2013.
triplex-2.1.tar.gz
triplex-1.2.tar.gz
algorithm.c.tat (alternative tables to look for T:A.T/T:A.A triplexes only)
libfasta-1.4.tar.gz (needed by triplex)
analyze_gff.sh prefilter_gff.c filter_gff.c count_scores.pl (to run triplex for all 8 types and generate statistics)
triplexfit.c (can only be compiled with hmmer-2.3.2, x86 binaries provided) triplexfit (x86) triplexfit (x86_64)
seqmix-0.2.tar.gz (used to prepare random, randomized and mixed sequences)
Sequences
E.coli (old) E.coli (new) Human
Random E.coli randomized Human randomized
Triplex-seeded Metalothionein-I triplex Inserted triplex sequences Inserted triplex sequences log
Results
(to view the data in Genome Browser, create a custom track at http://microbes.ucsc.edu/cgi-bin/hgGateway?db=eschColi_K12)
ecoli_0.001.gff ecoli_0.00001.gff ecoli_0.0000001.gff
Metalothionenin-I triplex
Links
web-based triplex search tool
MD calculations to predict isomorphic triplets

A dynamic programming algorithm for identification of triplex-forming sequences

Errata

Software

Sequences

Results

Links