RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.

ABSTRACT:

Motivation

Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression post-transcriptionally. A number of computational studies have so far been devoted to predicting joint secondary structures or binding sites under a specific class of interactions. In general, there is a trade-off between range of interaction type and efficiency of a prediction algorithm, and thus efficient computational methods for predicting comprehensive type of interaction are still awaited.

Results

We present RactIP, a fast and accurate prediction method for RNA-RNA interaction of general type using integer programming. RactIP can integrate approximate information on an ensemble of e

SUBMITTER: Kato Y 

PROVIDER: S-EPMC2935440 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature