NoFold: RNA structure clustering without folding or alignment.

ABSTRACT: Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences.

SUBMITTER: Middleton SA 

PROVIDER: S-EPMC4201820 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature