recipe mvp

detect creation/destruction of sequence motifs as a result of mutations






Sequence variation may cause the appearance or disappearance of certain motifs. Since motifs can be recognition sites for biological functions such as regulation or DNA modification, their gain and loss can have additional consequences. Using a list of variants in variant call format, the corresponding reference sequence, and a set of motifs to search for,mvp (motif-variant probe) identifies variants responsible for changing the number of occurrences of these motifs in the sequence. mvp can process both nucleotide and amino acid sequences.

package mvp

(downloads) docker_mvp



depends biopython:

depends pysam:


depends python:



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 mvp

and update with::

   mamba update mvp

To create a new environment, run:

mamba create --name myenvname mvp

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<tag>

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

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