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Monthly Downloads: 350
Programming language: Haskell
License: GNU General Public License v3.0 only
Latest version: v1.8.0

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README

RNAlien

RNAlien is a tool for automatic construction of RNAfamily models from a single sequence.

It is available as a commandline tool, for testing or construction of few sequences the webservice can be used.

The source code of RNAlien is open source and available via GitHub and Hackage (License GPL-3):

  • GitHub Build Status Hackage Bioconda Docker Repository on Quay

    RNAlien can be installed with all tool dependencies via conda. Once you have conda installed simply type:

     conda create -n rnalien -c bioconda -c conda-forge rnalien
    

    Activate the environment in which RNAlien was installed to use it:

     conda activate rnalien
    

    To use the offline-mode of the commandline tool additionally following database downloads are required:

    • Download NCBI Taxonomy Dump bash wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz tar -xzf new_taxdump.tar.gz
    • Download NCBI Blast version 5 database bash #After installing and activating the RNAlien bioconda environment use update_blastdb.pl #Show all available databases update_blastdb.pl --blastdb_version 5 --showall #Download the nt_v5 database (~about 70 GB in size) update_blastdb.pl --blastdb_version 5 nt_v5 --decompress

    Usage

    After installation with bioconda, activating the environment and downloading the files using the offline mode of the command line tool is recommended. Following are example calls for the files contained in the test directory of the repository. Using -c 4 and +RTS -N4 provides 4 cpu threads to the used tool dependencies (e.g. blast,..) and to RNAlien.

    • Single fasta input: bash RNAlien -i single.fa -c 4 -j -b /pathto/blast5db/nt_v5 -d single -w /pathto/new_taxdump/taxidlineage.dmp +RTS -N4
    • Multi fasta input:
       RNAlien -i testmulti.fa -c 4 -j -b /pathto/blast5db/nt_v5 -d single -w /pathto/new_taxdump/taxidlineage.dmp +RTS -N4
    
    • Stockholm alignment (with consensus structure) input bash RNAlien -p test.stockholm -c 4 -j -b /pathto/blast5db/nt_v5 -d aln -w /pathto/new_taxdump/taxidlineage.dmp +RTS -N4

    If you just want to try RNAlien out, or to construct a single family the onlinse mode can be used. It does not require database downloads and queries the required information from ncbi webservices. A stable, uninterupted internet connection is mandatory.

    • Single fasta input (online-mode): bash RNAlien -i single.fa -c 4 -d onsingle +RTS -N4 To display the possible commandline options run:
       RNAlien --help
    

    For detailed instruction how to use RNAlien please see the Help page.

TaxonomyTools which can be used to visualise the organisms included in a RNAlien result can be found here (License GPL-3):

  • GitHub Build Status Hackage


*Note that all licence references and agreements mentioned in the RNAlien README section above are relevant to that project's source code only.