recipe rnaclust

A tool for clustering of RNAs based on their secondary structures using LocARNA

Homepage:

http://www.bioinf.uni-leipzig.de/~kristin/Software/RNAclust/

License:

GPL / GPL-2.0

Recipe:

/rnaclust/meta.yaml

Links:

biotools: RNAclust

RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif. It requires as input a multiple FASTA file. In the first step for each input sequence the base pair probability matrix of its secondary structure distribution is calculated (using RNAfold from the Vienna RNA package). Secondly, for each pair of base pair probability matrices a sequence-structure alignment is calculated using LocARNA. Lastly, a hierarchical cluster-tree (in NEWICK format) is derived by WPGMA clustering of the pairwise alignment distances and the optimal number of clusters is calculated from the tree.

package rnaclust

(downloads) docker_rnaclust

versions:

1.3-0

depends libgcc:

depends locarna:

depends perl:

5.22.0*

depends viennarna:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install rnaclust

and update with::

   mamba update rnaclust

To create a new environment, run:

mamba create --name myenvname rnaclust

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/rnaclust:<tag>

(see `rnaclust/tags`_ for valid values for ``<tag>``)

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