selenoprofiles4 4.3.0

Gene finding pipeline for selenoprotein and selenocysteine machinery

selenoprofiles4

Gene finding pipeline for selenoprotein and selenocysteine machinery.

Installation

If you don't have conda, install it following these instructions.

Create a new dedicated enviroment called sp4, then activate it:

conda create -yn sp4
conda activate sp4

Install selenoprofiles4 and its dependencies in the sp4 environment:

conda install -c mmariotti -c anaconda -c bioconda -c biobuilds selenoprofiles4

If everything worked correctly, the selenoprofiles command is now available, but it is still not setup. Run this and follow instructions:

selenoprofiles -setup

Finally, run this to automically download the latest built-in profiles (github repo) to search for known selenoproteins and selenocysteine machinery:

selenoprofiles -download

You're ready to go! Remember to activate the sp4 environment everytime you run selenoprofiles.

Usage

For up-to-date usage information, run:

selenoprofiles -h

Bug report

Please report any bugs at the github issues page.

Citation

Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Mariotti M, Guigó R. Bioinformatics. 2010 Nov 1;26(21):2656-63. doi: 10.1093/bioinformatics/btq516