Gene finding pipeline for selenoprotein and selenocysteine machinery
Project description
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
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