LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.

Publication date: Aug 31, 2023

Many RNAs function through RNA-RNA interactions. Fast and reliable RNA structure prediction with consideration of RNA-RNA interaction is useful, however, existing tools are either too simplistic or too slow. To address this issue, we present LinearCoFold, which approximates the complete minimum free energy structure of two strands in linear time, and LinearCoPartition, which approximates the cofolding partition function and base pairing probabilities in linear time. LinearCoFold and LinearCoPartition are orders of magnitude faster than RNAcofold. For example, on a sequence pair with combined length of 26,190 nt, LinearCoFold is 86. 8cD7 faster than RNAcofold MFE mode, and LinearCoPartition is 642. 3cD7 faster than RNAcofold partition function mode. Surprisingly, LinearCoFold and LinearCoPartition’s predictions have higher PPV and sensitivity of intermolecular base pairs. Furthermore, we apply LinearCoFold to predict the RNA-RNA interaction between SARS-CoV-2 genomic RNA (gRNA) and human U4 small nuclear RNA (snRNA), which has been experimentally studied, and observe that LinearCoFold’s prediction correlates better with the wet lab results than RNAcofold’s.

Open Access PDF

Concepts Keywords
26190nt Algorithms
Fast Approximates
Lab Base
Rna Interacting
Slow Interaction


Type Source Name
disease VO time
drug DRUGBANK Tropicamide
disease VO USA
drug DRUGBANK Coenzyme M
pathway REACTOME Reproduction
disease IDO algorithm
drug DRUGBANK Tricyclazole
drug DRUGBANK Cysteamine
disease VO efficiency
drug DRUGBANK Tacrine
drug DRUGBANK Tretamine
drug DRUGBANK Pirenzepine
disease IDO process
drug DRUGBANK L-Threonine
disease MESH arc
drug DRUGBANK 3 7 11 15-Tetramethyl-Hexadecan-1-Ol
disease MESH arcs
drug DRUGBANK Dimercaprol
disease VO URE
disease IDO host
disease IDO history
drug DRUGBANK Huperzine B
disease MESH rous sarcoma
disease MESH neurological disorders
disease VO Bacteria
disease VO Archaea
disease VO efficient
drug DRUGBANK Lysozyme

Original Article

(Visited 1 times, 1 visits today)