• Downloading and Installing
    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.


    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]