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‎.gitignore

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bin/*
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tmp_rets/*
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*.pyc
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.vscode/*
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# Prerequisites
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*.d
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# Compiled Object files
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*.slo
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*.lo
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*.o
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*.obj
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# Precompiled Headers
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*.gch
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*.pch
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# Compiled Dynamic libraries
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*.so
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*.dylib
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*.dll
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# Fortran module files
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*.mod
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*.smod
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# Compiled Static libraries
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*.lai
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*.la
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*.a
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*.lib
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# Executables
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*.exe
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*.out
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*.app

‎Makefile

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################################
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# Makefile
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#
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# author: Sizhen
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# edited by: 10/2020
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################################
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CC=g++
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# DEPS=LinearPartitionDouble.h doublebp.cpp energy_parameter.h feature_weight.h intl11.h intl21.h intl22.h utility_v.h utility.h LinearFoldEval.cpp
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# DEPS=newbpLog.cpp LinearPartitionLog.h energy_parameter.h feature_weight.h intl11.h intl21.h intl22.h utility_v.h utility.h LinearFoldEval.cpp
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# DEPS=LinearPartitionNewprune-C.h energy_parameter.h feature_weight.h intl11.h intl21.h intl22.h utility_v.h utility.h LinearFoldEval.cpp newbp-C.cpp
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# DEPS=LinearPartitionNewprune.h energy_parameter.h feature_weight.h intl11.h intl21.h intl22.h utility_v.h utility.h LinearFoldEval.cpp
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# DEPS=newbpLog_pf_type.cpp LinearPartitionLog_pf_type.h energy_parameter.h feature_weight.h intl11.h intl21.h intl22.h utility_v.h utility.h LinearFoldEval.cpp
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# DEPS= LinearSampling.h energy_parameter.h feature_weight.h intl11.h intl21.h intl22.h utility_v.h utility.h
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DEPS=src/LinearTurboFold.h src/SeqFold.h src/LinearPartition/src/LinearPartition.h src/LinearAlignment/src/LinearAlign.h src/probknot.h \
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src/ConfigParser.h src/utils/common_utils.h src/utils/defines.h src/utils/structure_object.h \
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src/utils/ansi_string.h src/utils/utils.h src/utils/TProgressDialog.h src/utils/MultiSequence.h src/utils/SafeVector.h src/utils/Sequence.h \
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src/utils/structure.h src/utils/rna_library.h \
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src/utils/phmm_aln.h src/utils/phmm.h src/utils/p_alignment.h \
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src/utils/math/matrix.h src/utils/random.h \
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src/ProbabilisticModel.h src/Alignment.h src/utils/GuideTree.h
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CFLAGS=-std=c++11 -O3
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.PHONY : clean linearturbofold
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objects=bin/linearturbofold
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linearturbofold: src/LinearTurboFold.cpp $(DEPS)
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chmod +x linearturbofold
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mkdir -p bin
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$(CC) src/LinearTurboFold.cpp src/SeqFold.cpp src/LinearPartition/src/LinearPartition.cpp src/LinearAlignment/src/LinearAlign.cpp src/probknot.cpp \
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src/ConfigParser.cpp src/utils/common_utils.cpp src/utils/structure_object.cpp \
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src/utils/ansi_string.cpp src/utils/utils.cpp src/utils/TProgressDialog.cpp src/utils/MultiSequence.cpp src/utils/Sequence.cpp \
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src/utils/structure.cpp src/utils/rna_library.cpp \
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src/utils/phmm_aln.cpp src/utils/phmm.cpp src/utils/p_alignment.cpp \
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src/utils/math/matrix.cpp src/utils/random.cpp \
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src/ProbabilisticModel.cpp src/Alignment.cpp src/utils/GuideTree.cpp \
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$(CFLAGS) -Dlv -o bin/linearturbofold
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clean:
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-rm $(objects)

‎README.md

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# LinearTurboFold
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# LinearTurboFold
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This repository contains the C++ source code for the LinearTurboFold project, an end-to-end linear-time algorithm for structural alignment and conserved structure prediction of RNA homologs, which is the first joint-fold-and-align algorithm to scale to full-length SARS-CoV-2 genomes without imposing any constraints on base-pairing distance.
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[LinearTurboFold: Fast Folding and Alignment for RNA Homologs with Applications to Coronavirus](https://www.biorxiv.org/content/10.1101/2020.11.23.393488v2)
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Sizhen Li, He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David Mathews*, Liang Huang*
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\* corresponding author
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# Dependency
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gcc 4.8.5 or above; <br>
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python2.7
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# Compile
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```
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Make
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```
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# Run
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LinearTurboFold can be run with:
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```
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./linearturbofold -i input.fasta -o output_dir [OPTIONS]
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```
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The input file should be in the FASTA format. Please see [input.fasta](input.fasta) as an example. <br>
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Output a multiple sequence alignment and predicted secondary structures in the output directory.
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### OPTIONS
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`--it`
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The number of iterations (default 3). <br>
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`--b1`
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The beam size for LinearAlignment (default 100, set 0 for infinite beam). <br>
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`--b2`
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The beam size for LinearPartition (default 100, set 0 for infinite beam). <br>
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`--pf`
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Save partition functions for all the sequencs after the last iteration (default False). <br>
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`--bpp`
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Save base pair probabilities for all the sequencs after the last iteration (default False). <br>
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`-v`
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Print out alignment, folding and runtime information (default False). <br>
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`--th`
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Set ThreshKnot threshknot (default 0.3). <br>
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`--tkit`
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Set ThreshKnot iterations (default 1). <br>
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`--tkhl`
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Set ThreshKnot minimum helix length (default 3). <br>
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### Example
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```
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./linearturbofold -i input.fasta -o rets/ --pf --bpp
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100% [==================================================]
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3 iterations Done!
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Outputing partition functions to files ...
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Outputing base pair probabilities to files ...
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Outputing multiple sequence alignment to rets/output.aln...
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Outputing structures to files ...
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```
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# Evalutation Dataset
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We used the [RNAStralign](https://rna.urmc.rochester.edu/publications.html) dataset with known alignments and structures to evaluate LinearTurboFold and benchmarks.
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# SARS-CoV-2 Dataset and Results
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The 25 SARS-CoV-2 and SARS-related genomes analyzed in the paper are listed in [samples25.fasta](data/sars-cov-2_data/samples25.fasta). <br>
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For further study by experts,
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we provide the whole multiple sequence alignment and predicted structures for all genomes from LinearTurboFold in [sars-cov-2_and_sars-related_25_genomes_msa_structures.txt](sars-cov-2_rets/sars-cov-2_and_sars-related_25_genomes_msa_structures.txt). <br>
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Each genome corresponds to three lines: sequence name, aligned sequence and aligned structure, respectively.
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