This codebase replaces the now deprecated version: https://github.com/abentu0101/LinearFold. This version fixes many bugs and design problems in the old version.

LinearFold: Linear-Time Prediction for RNA Secondary Structures

This repository contains the C++ source code for the LinearFold project, the first linear-time prediction algorithm/software for RNA secondary structures.

LinearFold: Linear-Time Approximate RNA Folding by 5’-to-3’ Dynamic Programming and Beam Search. Bioinformatics, Volume 35, Issue 14, July 2019, Pages i295–i304. ISMB 2019

Liang Huang*, He Zhang**, Dezhong Deng**, Kai Zhao, Kaibo Liu, David Hendrix, David Mathews

* corresponding author

** contributed equally

Web server: http://linearfold.org

Dependencies

GCC 4.8.5 or above; python3

To Compile

make

To Run

The LinearFold parser can be run with:

echo SEQUENCE | ./linearfold [OPTIONS]

OR

cat SEQ_OR_FASTA_FILE | ./linearfold [OPTIONS]

Both FASTA format and pure-sequence format are supported for input.

OPTIONS:

--beamsize BEAM_SIZE or -b BEAM_SIZE

The beam size (default 100). Use 0 for infinite beam.

--Vienna or -V

Switches LinearFold-C (by default) to LinearFold-V.

--fasta

Specify that the input is in fasta format. (default FALSE)

--verbose or -v

Prints out energy of each loop in the structure. (default False)

--sharpturn

Enable sharpturn in prediction. (default False)

--eval

Enable eval mode, which can calculate free energy for a given structure of a sequence. (default False)

--constraints

Enable adding specific constraints in prediction (default False). The constraint sequence should have the same length as the RNA sequence. "? . ( )" indicates a position for which the proper matching is unknown, unpaired, left or right parenthesis respectively. The parentheses must be well-banlanced and non-crossing.

--zuker

output Zuker suboptimal structures, (DEFAULT=FALSE)

--delta

compute Zuker suboptimal structures with scores or energies(-V, kcal/mol) in a centain range of the optimum, (DEFAULT=5.0)

--shape <filename>

use SHAPE reactivity data to guide structure predictions
Please refer to this link for the SHAPE data format: https://rna.urmc.rochester.edu/Text/File_Formats.html#SHAPE

--dangles INT or -d INT

the way to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops, (only supporting 0 or 2, DEFAULT=2)
--dangles 0, ignores dangling ends
--dangles 2, dangling energies are added for the bases adjacent to a helix on both sides in any case

To Visualize

LinearFold is able to visualize the structure using a circular plot.

To draw a circular plot, run command:

cat TARGET_FILE | ./draw_circular_plot

TARGET_FILE contains one sequence and its structure; see "ecoli_tRNA" file as an example.

Example Run Predict

cat testseq | ./linearfold
UGAGUUCUCGAUCUCUAAAAUCG
....................... (-0.22)
AAAACGGUCCUUAUCAGGACCAAACA
.....((((((....))))))..... (4.91)
AUUCUUGCUUCAACAGUGUUUGAACGGAAU
.............................. (-0.29)
UCGGCCACAAACACACAAUCUACUGUUGGUCGA
(((((((...................))))))) (0.99)
GUUUUUAUCUUACACACGCUUGUGUAAGAUAGUUA
.....(((((((((((....))))))))))).... (6.66)

echo GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA | ./linearfold -V -b 20
GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA
(((((((..((((.......))))((((((((...)))))))).(((((.......)))))))))))).... (-31.50)

Example Run Predict with constraints

cat testcons | ./linearfold --constraints
AACUCCGCCAGGCCUGGAAGGGAGCAACGGUAGUGACACUCUCUGUGUGCGUAGGUUGCCUAGCUACCAUUU
??(???(??????)?(????????)???(??????(???????)?)???????????)??.???????????
..(.(((......)((........))(((......(.......).))).....))..).............. (-27.33)
GCCUGGUGACCAUAGCGAGUCGGUACCACCCCUUCCCAUCCCGAACAGGACCGUGAAACGACUCCGCGCCGAUGAUAGUGCGGAUUCCCGUGUGAAAGUAGGUCAUCGCCAGGC
??(??(???(??????)???????????????(????)???(???????????(??(????.)??????????(??????)?)??????)????????????)????????)??
(((((((..(......).........(((...(....)...((....(((...(..(.....)..........(......).)..))))).))).......))))......))) (-44.00)

echo -e "GAACCCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGU\n??????????????????(????????????????)" | ./linearfold --constraints
GAACCCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGU
??????????????????(????????????????)
..................(................) (-8.85)

echo -e "GAACCCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGU\n??????????????????(????????????????)" | ./linearfold --constraints -V
GAACCCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGU
??????????????????(????????????????)
.....(((.......)))(.....((....))...) (3.70)

Example Run Predict and output suboptimal structures

echo GCCUGGUGACCAUAGCGAGUCGGUACCACCCCUUCCCAUCCCGAACAGGACCGUGAAACGACUCCGCGCCGAUGAUAGUGCGGAUUCCCGUGUGAAAGUAGGUCAUCGCCAGGC | ./linearfold -V --zuker --delta 2.0
(((((((((.....((((((((....(((.(((((.......))..)))...)))...)))))).))(((.........((((....)))).........)))..))))))))) (-35.50)
Zuker suboptimal structures...
(((((((((.....((((((((....(((.(((((.......))..)))...)))...)))))).))(((.........((((....)))).........)))..))))))))) (-35.50)
(((((((((.....((((((((....(((.(((((.......))..)))...)))...)))))).))(((.((......((((....))))......)).)))..))))))))) (-35.40)
(((((((((.....((((((((....(((....(((...........)))..)))...)))))).))(((.........((((....)))).........)))..))))))))) (-34.90)
(((((((((.....((((((((....(((.(((((.......))..)))...)))...)))))).))(((.((..(..(((((....)))))..)..)).)))..))))))))) (-34.70)
(((((((((((.....((((((....(((.(((((.......))..)))...)))...))))))(((((........)))))..................))))...))))))) (-34.50)
(((((((((((.....((((((....(((.(((((.......))..)))...)))...))))))(((((........)))))..(((......)))....))))...))))))) (-34.40)
(((((((((.......((((((....(((.(((((.......))..)))...)))...))))))(((((........)))))((((..(........)..)))).))))))))) (-34.20)
(((((((((((...((((((((....(((.(((((.......))..)))...)))...)))))((((((........)))))).....))).........))))...))))))) (-34.00)
(((((((((((...((((((((....(((.(((((.......))..)))...)))...))))))(((((........)))))...............)).))))...))))))) (-33.90)
(((((((((.....((((((((.(((..((..(((.......)))..))...)))...)))))).))(((.........((((....)))).........)))..))))))))) (-33.70)
(((((((((.....((((((((....(((.........(((......)))..)))...)))))).))(((.........((((....)))).........)))..))))))))) (-33.70)
(((((((((.......((((((....(((.(((((.......))..)))...)))...))))))(((((........))))).....((...........))...))))))))) (-33.60)

Example Run SHAPE-guided structure prediction

echo GCCUGGUGACCAUAGCGAGUCGGUACCACCCCUUCCCAUCCCGAACAGGACCGUGAAACGACUCCGCGCCGAUGAUAGUGCGGAUUCCCGUGUGAAAGUAGGUCAUCGCCAGGC | ./linearfold -V --shape example.shape
GCCUGGUGACCAUAGCGAGUCGGUACCACCCCUUCCCAUCCCGAACAGGACCGUGAAACGACUCCGCGCCGAUGAUAGUGCGGAUUCCCGUGUGAAAGUAGGUCAUCGCCAGGC
((((((........((((((((.(((............(((......)))..)))...))))).)))..(((((((..(((...(((......))).))).))))))))))))) (-66.30)

Example Run Predict (-d0 option: ignoring dangling ends)

echo GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA | ./linearfold -V -d0
GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA
(((((((..((((.......))))((((((((...)))))))).(((((.......)))))))))))).... (-25.50)

Example Run Eval

cat testeval | ./linearfold --eval
UGAGUUCUCGAUCUCUAAAAUCG
.(((........)))........ (-1.80)
AAAACGGUCCUUAUCAGGACCAAACA
.....((((((....))))))..... (-9.30)
AUUCUUGCUUCAACAGUGUUUGAACGGAAU
(((((...(((((......))))).))))) (-6.80)
UCGGCCACAAACACACAAUCUACUGUUGGUCGA
(((((((((..............))).)))))) (-7.80)
GUUUUUAUCUUACACACGCUUGUGUAAGAUAGUUA
....((((((((((((....))))))))))))... (-13.00)

echo -e "GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA\n(((((((..((((.......))))((((((((...)))))))).(((((.......))))))))))))....\n" | ./linearfold --eval --verbose
Hairpin loop ( 13, 21) CG : 4.50
Interior loop ( 12, 22) UA; ( 13, 21) CG : -2.40
Interior loop ( 11, 23) AU; ( 12, 22) UA : -1.10
Interior loop ( 10, 24) GC; ( 11, 23) AU : -2.40
Hairpin loop ( 32, 36) UA : 5.90
Interior loop ( 31, 37) UA; ( 32, 36) UA : -0.90
Interior loop ( 30, 38) CG; ( 31, 37) UA : -2.10
Interior loop ( 29, 39) CG; ( 30, 38) CG : -3.30
Interior loop ( 28, 40) UA; ( 29, 39) CG : -2.40
Interior loop ( 27, 41) UA; ( 28, 40) UA : -0.90
Interior loop ( 26, 42) CG; ( 27, 41) UA : -2.10
Interior loop ( 25, 43) GC; ( 26, 42) CG : -3.40
Hairpin loop ( 49, 57) GC : 4.40
Interior loop ( 48, 58) GC; ( 49, 57) GC : -3.30
Interior loop ( 47, 59) GC; ( 48, 58) GC : -3.30
Interior loop ( 46, 60) UA; ( 47, 59) GC : -2.10
Interior loop ( 45, 61) CG; ( 46, 60) UA : -2.10
Multi loop ( 7, 62) GC : 1.40
Interior loop ( 6, 63) CG; ( 7, 62) GC : -2.40
Interior loop ( 5, 64) UA; ( 6, 63) CG : -2.40
Interior loop ( 4, 65) CG; ( 5, 64) UA : -2.10
Interior loop ( 3, 66) GU; ( 4, 65) CG : -2.50
Interior loop ( 2, 67) GC; ( 3, 66) GU : -1.50
Interior loop ( 1, 68) GC; ( 2, 67) GC : -3.30
External loop : -1.70
GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA
(((((((..((((.......))))((((((((...)))))))).(((((.......)))))))))))).... (-31.50)

Example: Draw Circular Plot

cat ecoli_tRNA | ./draw_circular_plot

linearfold / linearfold Goto Github PK

linearfold's Introduction

LinearFold: Linear-Time Prediction for RNA Secondary Structures

Dependencies

To Compile

To Run

To Visualize

Example Run Predict

Example Run Predict with constraints

Example Run Predict and output suboptimal structures

Example Run SHAPE-guided structure prediction

Example Run Predict (-d0 option: ignoring dangling ends)

Example Run Eval

Example: Draw Circular Plot

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