Triplex search software suite
Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand in its major groove.
This sequence-specific process offers a potent mechanism for targeting genomic loci of interest,
that is of great interest for bio-technological and gene-therapeutic applications.
For a review on the potential in vivo roles of nucleic acid triplex formation we
refer to our manuscript
published in "RNA biology".
Triplex-formation requires a duplex, presumably DNA, and a single-stranded nucleotide
sequence acting as the third strand, presumably RNA:
The process of predicting putative triplexes in sequence data can be divided into three steps
- identifying the triplex-forming oligonucleotides (TFO) in single-stranded sequences
- identifying the triplex target sites in double-stranded sequences able to accomondate a third strand
- assessing the compatibility of potential TFO/TTS pairs according to the canonical triplex formation rules
Here, we present Triplexator
an efficient computational framework that addresses all three aspects of triplex-formation.
employs approximate pattern matching based on the
triplex formation rules
in order to find putative TFO/TTS pairs (triplexes)
in two sets of nucleotide sequences, where one set contains the duplex sequences
and the other the single-stranded partner.
is implemented in C++ and leverages data-structures and functionalty
from the Sequence Analysis template library (SeqAn)
You can download Triplexator
, consult the manual
or check out some examples
Fabian A. Buske et al.
, "Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data", Genome Res
, 2012, 22, 1372-1381, Pubmed