The website RNA StrAT (RNA Structure Analysis Toolkit) was carried out by Valentin Guignon initialy within the framework of its Master of bioinformatics (M.Sc.) at University of Montreal under the direction of Sylvie Hamel and the joint management of Cedric Chauve. Its developpment was prosecuted depending on the available free time and various helps. Thus, Jean-Philippe Goulet participated in the elaboration of alignments display during his internship in the DIRO and Louis-Philippe Lavoie provided a precious help to import secondary structures from PDB files.


The majority of the tools presented here result from our work, nevertheless certain tools come from authors external of this site:


The secondary structures of our database come from external sources and are mainly imported from the RFam1. When elements are imported from a multiple alignment having a consensus structure, the structure of each sequence is built starting from the consensus according to the procedure described here.

Quotations and references

If you use this site for your work, thanks to provide the website address (www-lbit.iro.umontreal.ca/rnastrat) in your publications and to quote the following paper:
V.Guignon, C.Chauve and S.Hamel, An edit distance between RNA stem-loops, Lecture Notes in Computer Science 3772 (String Processing and Information REtrival), pp. 335-347, 2005.

Do not forget to also mention the papers which provided the data you used. With regard to the data resulting from RFam, you can refer to this page.

If you wish to link our site or to incorporate on your site the contents of some pages, we will be very grateful if you include with the link the key-words "RNA secondary structure comparison and alignment" and that you also add one of our logos:
RNAStrat or RNAStrat or RNAStrat

For example:

RNAStrat Tools for comparison
and alignment of
secondary structures of RNA

HTML Code:

  1. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., Eddy, S.R., RFam: an RNA family database, Nucleic Acids Research, 2003, 31, 1, 439-441.
  2. Ivo L. Hofacker, Vienna RNA Package.