LinearPartition: Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities
This repository contains the C++ source code for the LinearPartition project, the first linear-time partition function and base pair probabilities calculation algorithm/software for RNA secondary structures.
LinearPartition: Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities
He Zhang, Liang Zhang, David Mathews, Liang Huang*
* corresponding author
gcc 4.8.5 or above; python2.7
make
LinearPartition can be run with:
echo SEQUENCE | ./linearpartition [OPTIONS]
OR
cat SEQ_OR_FASTA_FILE | ./linearpartition [OPTIONS]
Both FASTA format and pure-sequence format are supported for input.
OPTIONS:
-b BEAM_SIZE
The beam size (default 100). Use 0 for infinite beam.
-V
Switches LinearPartition-C (by default) to LinearPartition-V.
--verbose
Prints out beamsize, Log Partition Coefficient or free energy of ensemble (-V mode) and runtime information. (default False)
--sharpturn
Enable sharpturn. (default False)
-o
Outputs base pairing probability matrix to a file with user specified name. (default False)
--prefix
Outputs base pairing probability matrices to files with user specified prefix. (default False)
-p
Partition function calculation only. (default False)
cat testseq | ./linearpartition -V --prefix testseq_output
UGAGUUCUCGAUCUCUAAAAUCG
Free Energy of Ensemble: -1.96 kcal/mol
Outputing base pairing probability matrix to testseq_output_1...
Done!
AAAACGGUCCUUAUCAGGACCAAACA
Free Energy of Ensemble: -9.41 kcal/mol
Outputing base pairing probability matrix to testseq_output_2...
Done!
AUUCUUGCUUCAACAGUGUUUGAACGGAAU
Free Energy of Ensemble: -7.72 kcal/mol
Outputing base pairing probability matrix to testseq_output_3...
Done!
UCGGCCACAAACACACAAUCUACUGUUGGUCGA
Free Energy of Ensemble: -9.09 kcal/mol
Outputing base pairing probability matrix to testseq_output_4...
Done!
GUUUUUAUCUUACACACGCUUGUGUAAGAUAGUUA
Free Energy of Ensemble: -13.58 kcal/mol
Outputing base pairing probability matrix to testseq_output_5...
Done!
echo GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA | ./linearpartition -o output
GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA
Log Partition Coefficient: 15.88268
Partition Function Calculation Time: 0.004343 seconds.
Base Pairing Probabilities Calculation Time: 0.003293 seconds.
Outputing base pairing probability matrix to output...
Done!
echo GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA | ./linearpartition -V -p --verbose
beam size: 100
GGGCUCGUAGAUCAGCGGUAGAUCGCUUCCUUCGCAAGGAAGCCCUGGGUUCAAAUCCCAGCGAGUCCACCA
Free Energy of Ensemble: -32.14 kcal/mol
Partition Function Calculation Time: 0.005509 seconds.
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