Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions.

ABSTRACT:

Background

Many regulatory non-coding RNAs (ncRNAs) function through complementary binding with mRNAs or other ncRNAs, e.g., microRNAs, snoRNAs and bacterial sRNAs. Predicting these RNA interactions is essential for functional studies of putative ncRNAs or for the design of artificial RNAs. Many ncRNAs show clear signs of undergoing compensating base changes over evolutionary time. Here, we postulate that a non-negligible part of the existing RNA-RNA interactions contain preserved but covarying patterns of interactions.

Methods

We present a novel method that takes compensating base changes across the binding sites into account. The algorithm works in two steps on two pre-generated multiple alignments. In the first step, individual base pairs with high reliability are found u

SUBMITTER: Seemann SE 

PROVIDER: S-EPMC2903599 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature