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apt-get install predictprotein $ apt-get install predictprotein
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Running this example will take a few minutes:
$ predictprotein --seqfile /usr/share/doc/predictprotein/examples/tquick.fasta --output-dir /tmp/pp
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 * [[https://rostlab.org/owiki/index.php/PredictProtein_-_Documentation|PredictProtein Documentation]]

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This page will help you get started with PredictProtein for Debian and derivatives, e.g. Bio-Linux. Detailed documentation of PredictProtein is available at the Rost Lab.


$ apt-get install predictprotein


PredictProtein needs databases to function. The easiest and most convenient is to download these as a compressed archive from the PredictProtein web site. All of the databases in the archive are available publicly, the archive is provided for convenience only. The link to the database archive download is hidden until you click 'Click here to download a Debian based image'. Read man predictprotein if you want to choose your databases.

# You will need up to 30GB free space in ${YOUR_DATA_ROOT}/rostlab-data
$ wget 'http://www.rostlab.org/services/ppmi/download_file?format=gzip&file_to_download=db' --continue -O /tmp/rostlab-data.txz
$ mkdir -p ${YOUR_DATA_ROOT}/rostlab-data && tar -xvJf /tmp/rostlab-data.txz -C ${YOUR_DATA_ROOT}/rostlab-data


Default configuration is in /usr/share/predictprotein/predictproteinrc.default.

Create /etc/predictproteinrc with these values (replace ${YOUR_DATA_ROOT} with the actual value):

# Override default predictprotein configuration in /usr/share/predictprotein/predictproteinrc.default with these values:

Test run

Running this example will take a few minutes:

$ predictprotein --seqfile /usr/share/doc/predictprotein/examples/tquick.fasta --output-dir /tmp/pp

See also