RNA-align standalone package
RNA-align is a free and open-source RNA and DNA structure alignment program written in C++ (Read more).
- Download RNA-align source code. You need g++ to compile RNA-align:
$ g++ -O3 -ffast-math -o RNAalign RNAalign.cpp -static
$ make clean; make RNAalign
The "-static" flag should be deleted on Mac, which does not support static build.
- Download pre-compiled executable for 64bit Linux. Nevetheless, it is recommended that you download the source code and compile it on your machine, which gives higher speed to run the program.
RNA-align benchmark datasets
RNA secondary structure (SS) assignment and file format conversion
These programs are not required for RNA-align to work. They are provided to allow reproduction of SS assignment results reported in the RNA-align paper.
[Back to RNA-align homepage]
- Download pre-compiled executable for the subroutine of coarse-grain SS assignment used in RNA-align. The source code of this program is available as part of the RNA-align source code and can be separately compiled by
Assign SS for PDB file 'pdb.pdb' by
- Download source code for our reference implement of full-atomic SS assignment based on angles and distances of atoms involved in hydrogen bond formation in base pairs. Assign SS for PDB file 'pdb.pdb' by
$ python ./3Dto2D.py pdb.pdb
- Download source code for the subroutine used by RNA-align server to converting mmCIF/PDBx format into PDB format. Compile the program with:
Convert PDBx/mmCIF file 'pdb.cif' into PDB format by:
$ ./cif2pdb pdb.cif > pdb.pdb