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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.
Installation
$ apt-get install predictprotein
Databases
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
Configuration
Default configuration is in /usr/share/predictprotein/predictproteinrc.default.
Create /etc/predictproteinrc with these values (replace ${YOUR_DATA_ROOT} with the actual value):
# Override default predictprotein configuration in /usr/share/predictprotein/predictproteinrc.default with these values:
[predictprotein]
bigblastdb=${YOUR_DATA_ROOT}/rostlab-data/data/big/big
big80blastdb=${YOUR_DATA_ROOT}/rostlab-data/data/big/big_80
prositedat=${YOUR_DATA_ROOT}/rostlab-data/data/prosite/prosite.dat
prositeconvdat=${YOUR_DATA_ROOT}/rostlab-data/data/prosite/prosite_convert.dat
swissblastdb=${YOUR_DATA_ROOT}/rostlab-data/data/swissprot/uniprot_sprot
pfam2db=${YOUR_DATA_ROOT}/rostlab-data/data/pfam_legacy/Pfam_ls
pfam3db=${YOUR_DATA_ROOT}/rostlab-data/data/pfam/Pfam-A.hmm
spkeyidx=${YOUR_DATA_ROOT}/rostlab-data/data/swissprot/keyindex_loctree.txt
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