Table of Contents

PANNZER2/SANSPANZ

Description

PANNZER2/SANSPANZ is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and gene ontology (GO) classes.

License

Pannzer has been published with the GNU Public Licence v3.

Usage

In puhti SANSPANZ annotation tool is taken in use with command:

module load biokit

After loading the module you can launch sanspanz analysis using command runsanspanz.py. For example:

runsanspanz.py -R -m Pannzer -s "species name" -i  input_seqs.fasta -o results.csv

The species name is used to determine taxonomic distances. The output is written to the file defined with option -o. Also three other output files are created: * Pannzer.out_1 contains details of the description (DE) prediction. * Pannzer.out_2 contains details of the GO prediction. * Pannzer.out_3 is a summary of all predicted annotations.

Pannzer.out_3 can be converted to HTML-format with command anno2html.pl:

anno2html.pl < Pannzer.out_3 > annotations.html

If you upload this file to Allas with command:

a-flip annotations.html

You can use the link provided by a-flip to study the results with your browser.

Note, that in Puhti you should always use runsanspanz.py with option -R that sends the analysis jobs to the annotation sever maintained by the Holm group. Thus, the job does not use the resources of Puhti and it can be run as an intercative job in a login node.

More information

For more information, execute command:

runsanspanz.py -h

Or study Pannzer home page:

Last edited Mon Apr 20 2020