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:

1. identifying the triplex-forming oligonucleotides (TFO) in single-stranded sequences
2. identifying the triplex target sites in double-stranded sequences able to accomondate a third strand
3. 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.

Triplexator 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.

Triplexator 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