This is my own version of RNAstructure, which includes tools for RNA secondary structure prediction and analysis.
It is provided to you under the GNU GPL, which is spelled out in gpl.txt.
In order to make the programs in the package run properly, please change the DATAPATH environment variable.
In BASH, this is accomplished with:
export DATAPATH=[directory in which RNAstructure resides]/RNAstructure/data_tables/
In CSH, this is accomplished with:
setenv DATAPATH [directory in which RNAstructure resides]/RNAstructure/data_tables/
I contributed several parts to RNAstructure, they are:
Under RNAstructure/ directory, please run:
make dynalign_ii
The executable dynalign_ii will be in the RNAstructure/exe/ directory.
The example configuration file to run Dynalign II on is RNAstructure/examples/dynalign_ii_sample.conf. Please run:
../exe/dynalign_ii dynalign_ii_sample.conf
in RNAstructure/examples/ directory.
Detailed instructions can be found at <http://rna.urmc.rochester.edu/Text/dynalign.html>. Reference article can be found at <http://nar.oxfordjournals.org/content/42/22/13939>.
Under RNAstructure/ directory, please run:
make Multifind
The executable Multifind will be in the RNAstructure/exe/ directory.
The example configuration file to run Multifind on is RNAstructure/examples/Multifind_sample.conf
Please run:
../exe/Multifind Multifind_sample.conf
in RNAstructure/examples/ directory.
Detailed instructions can be found at <http://rna.urmc.rochester.edu/Text/Multifind.html>. Reference article can be found at <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130200>.
Under RNAstructure/ directory, please run:
make conserved_training
The executable conserved_training will be in the RNAstructure/exe/ directory.
The example configuration file to run conserved_training on is RNAstructure/conserved_training/conserved_training.conf
Please run:
../exe/conserved_training conserved_training.conf
in RNAstructure/conserved_training/ directory.
The TrainingFiles field of the conf file should include the names of the pairwise alignment fasta file and the structure ct files for every data point in the training set. The TestingFiles field of the conf file should include the names of the pairwise alignment fasta file and the structure ct files for every data point in the testing set. The Alpha field of the conf file is the parameter for the L2 regularization.
Reference article can be found at <https://github.com/franfyh/RNAstructure/blob/master/maximum_entropy.pdf>.
The improvement of TurboFold is a project ongoing. Original TurboFold can be downloaded at <http://rna.urmc.rochester.edu/RNAstructure.html>. The reference of the original TurboFold can be found at <http://www.biomedcentral.com/1471-2105/12/108>.