DOWNLOAD and collaborate on StructRNAfinder development by accessing in our
GitHub account. All information to install and run it can be accessed there.
Installing the stand-alone version: (Only for linux)
To see more details related to the installation process please see the INSTALL file.
To install structRNAfinder and its requirements, type in a terminal located in structRNAfinder folder:
sudo sh install.sh
And follow the provided instructions.
Pre-Requisites:
StructRNAfinder uses third-part softwares and in-house Perl scripts in order to perform all its workflow. All them are automatically installed and configured when installing the tool. Bellow a list of softwares necessary to use it.
Documentation and Tutorial:
A complete documentation can be accessed and downloaded in our
GitHub account. Also, there is a complete
Tutorial showing two usage case and its results.
Here are all the options that the stand-alone version of StructRNAfinder has (
*Obligatory):
-i, --input input file in format fasta
*
-d, --database input reference database
*
-x, --otherDB define only if you are using a reference database different to Rfam [default: false]
-m, --method method to search for structural RNAs in a sequence dataset, cmscan or cmsearch [default: cmscan]
-r, --report report all annotated RNAs, for default only is showed the best hit per sequence [default: False]
-t, --tblout save parseable hits table to tab delimited file [default: <input>.tab]
-o, --output save alignment output to file [default: <input>.out]
-c, --cpu number of parallel CPU workers to use for multithreads [default: 1 cpu]
-p, --posStrand only search the positive strand [default: false]
-n, --negStrand only search the negative strand [default: false]
Options controlling inclusion (significance) thresholds (choose only one):
-e, --e-value maximun e-value to each hit [default: 0.01]
-s, --score minimun score to each hit [default: 10]
