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 and methods that provide both alignment and structure prediction. TurboFold II has comparable alignment accuracy with MAFFT and higher accuracy than other tools. TurboFold II also has comparable structure prediction accuracy as the original TurboFold algorithm, which is one of the most accurate methods. TurboFold II is part of the RNAstructure software package, which is freely available for download at http://rna.urmc.rochester.edu under a GPL license.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Tan Z,Fu Y,Sharma G,Mathews DHdoi
10.1093/nar/gkx815subject
Has Abstractpub_date
2017-11-16 00:00:00pages
11570-11581issue
20eissn
0305-1048issn
1362-4962pii
4259020journal_volume
45pub_type
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