Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.

ABSTRACT: Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method.

SUBMITTER: Fu Y 

PROVIDER: S-EPMC4267632 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature