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q-bio.BM2023
LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs
Sizhen Li, Ning Dai, He Zhang +3
The classical Sankoff algorithm for the simultaneous folding and alignment of homologous RNA sequences is highly influential, but it suffers from two major limitations in efficienc…
q-bio.BM2022
LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules
He Zhang, Sizhen Li, Liang Zhang +2
Many ncRNAs function through RNA-RNA interactions. Fast and reliable RNA structure prediction with consideration of RNA-RNA interaction is useful. Some existing tools are less accu…
q-bio.BM2022★ 1 cited
LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments
Apoorv Malik, Liang Zhang, Milan Gautam +5
Predicting the consensus structure of a set of aligned RNA homologs is a convenient method to find conserved structures in an RNA genome, which has many applications including vira…