Skip to content
Integer programming based prediction of RNA secondary structures with pseudoknots
C++ C Objective-C Shell Makefile CMake Other
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
cmake
m4
src
utils
.gitignore
AUTHORS
CMakeLists.txt
COPYING
Makefile.am
Makefile.in
README.md
aclocal.m4
compile
config.h.in
configure
configure.ac
depcomp
install-sh
missing
stamp-h1

README.md

IPknot for predicting RNA pseudoknot structures using integer programming

Requirements

Install

For GLPK,

./configure --with-vienna-rna=/path/to/vienna-rna --with-glpk

For Gurobi,

./configure --with-vienna-rna=/path/to/vienna-rna --with-gurobi=/path/to/gurobi

For CPLEX,

./configure --with-vienna-rna=/path/to/vienna-rna --with-cplex \
            --with-cplex-include=/path/to/cplex/include \
	        --with-cplex-lib=/path/to/cplex/lib

Usage

IPknot can take FASTA formatted RNA sequences as input, the predict their secondary structures including pseudoknots.

% ipknot: [options] fasta
 -h:       show this message
 -t th:    threshold of base-pairing probabilities for each level
 -g gamma: weight for true base-pairs equivalent to -t 1/(gamma+1)
           (default: -g 4 -g 8)
 -m:       use McCaskill model (default: CONTRAfold model)
 -i:       allow isolated base-pairs
 -b:       output the prediction via BPSEQ format

% ipknot ASE00001.fa
> ASE_00001
gaggaaagucccgccUCCAGAUCAAGGGAAGUCCCGCGAGGGACAAGGGUAGUACCCUUGGCAACUGCACAGAAAACUUACCCCUAAAUAUUCAAUGAGGAUUUGAUUCGACUCUUACCUUGGCGACAAGGUAAGAUAGAUGAAGAGAAUAUUUAGGGGUUGAAACGCAGUCCUUCCCGGAGCAAGUAGGGGGGUCAAUGAGAAUGAUCUGAAGACCUCCCUUGACGCAUAGUCGAAUCCCCCAAAUacagaagcgggcuua
.....(((.(((((.((........[[(([[[[[[..((]]]](((((((...)))))))...(((((...........((((((((((((((..............((...((((((((((....))))))))))..))......))))))))))))))......))))).]]))]]...[[....(((((((((....(((....)))...))))))))).(((]]...)))...))...........)).)))))))).

References

  • Sato, K., Kato, Y., Hamada, M., Akutsu, T., Asai, K.: IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming, Bioinformatics, 27(13):i85-i93 (Jul. 2011)
You can’t perform that action at this time.