TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.

ABSTRACT: This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions between all pairs of input sequences are iteratively estimated in TurboFold II by incorporating information from both the sequence identity and secondary structures. A multiple sequence alignment is obtained from these probabilities by using a probabilistic consistency transformation and a hierarchically computed guide tree. To assess TurboFold II, its sequence alignment and structure predictions were compared with leading tools, including methods that focus on alignment alone

SUBMITTER: Tan Z 

PROVIDER: S-EPMC5714223 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature