Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.

ABSTRACT:

Background

Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings.

Results

Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. I

SUBMITTER: Warris S 

PROVIDER: S-EPMC3895842 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature