De Novo Secondary Structure Motif Discovery Using RNAProfile

We describe here how conserved secondary structure motifs shared by functionally related RNA sequences can be detected through the software tool RNAProfile. RNAProfile takes as input a set of unaligned RNA sequences expected to share a common motif, and outputs the regions that are most conserved throughout the sequences, according to a similarity measure that takes into account both the sequence of the regions and the secondary structure they can form according to base-pairing and thermodynamic rules.
Source: Springer protocols feed by Bioinformatics - Category: Bioinformatics Source Type: news