Tfold, an algorithm for predicting non-coding RNA secondary structures

Fariza Tahi

Non - coding RNA play important roles in the regulation of biological
processes . Determining the structure of an RNA is a very important task .
Tere are experimental methods for this purpose , such as crystallography ,
NMR , etc . But because the high cost ( in time and money ) of these
experimental methods , in silico methods are largely required by
biologists . However , creating three - dimensional ( 3 D ) structural models of
RNA remains a big challenge and very few solutions are proposed in the
literature . On the other hand , several in silico methods are proposed for
predicting the secondary structure of RNA . There are methods using single
RNA sequence and methods using multiple sequences .
We propose an algorithm called Tfold , for predicting non - coding RNA
secondary structures , which uses several sequences . Tfold takes as input a
RNA sequence for which the secondary structure is searched , and a set of
aligned homologous sequences . It combines criteria of stability ,
conservation and covariation in order to search for stems . Stems are
searched recursively , from the most stable to the less stable ones . Tfold
searches for pseudo - knots , whatever their type . The developed tool , which
offers several possibilities of using , is available on the web site :
http : // tfold . ibisc . univ - evry . fr / TFold .