Activating Phobius/SignalP/TMHMM analyses

By default the Phobius, SignalP and TMHMM member database analyses are deactivated because they contain licensed components. In order to activate these analyses please obtain the relevant license and files from the provider (ensuring the software version numbers are the same as those supported by your current InterProScan installation).

An example of how to activate the Phobius 1.01, SignalP 4.1 and TMHMM 2.0 analyses with InterProScan 5.19-58.0 is given below. Files can be placed in any location as long as your interproscan.properties configuration is updated accordingly.

Phobius

Website: http://phobius.sbc.su.se/data.html

Files required by InterProScan:

  • bin/phobius/1.01/decodeanhmm

  • bin/phobius/1.01/phobius.model

  • bin/phobius/1.01/phobius.options

  • bin/phobius/1.01/phobius.pl

Example inteproscan.properties configuration:

phobius.signature.library.release=1.01
binary.phobius.pl.path=bin/phobius/1.01/phobius.pl

SignalP

Website: http://www.cbs.dtu.dk/services/SignalP/

For academic users there is a download site at: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp Other users are requested to contact software@cbs.dtu.dk.

Files required by InterProScan:

  • bin/signalp/4.1/signalp

  • bin/signalp/4.1/bin/nnhowplayer.Linux_i386

  • bin/signalp/4.1/bin/nnhowplayer.Linux_i486

  • bin/signalp/4.1/bin/nnhowplayer.Linux_i586

  • bin/signalp/4.1/bin/nnhowplayer.Linux_i686

  • bin/signalp/4.1/bin/nnhowplayer.Linux_ia64

  • bin/signalp/4.1/bin/nnhowplayer.Linux_x86_64

Example inteproscan.properties configuration:

signalp_euk.signature.library.release=4.1
signalp_gram_positive.signature.library.release=4.1
signalp_gram_negative.signature.library.release=4.1
binary.signalp.path=bin/signalp/4.1/signalp
signalp.perl.library.dir=bin/signalp/4.1/lib

Please confirm that the following line in the “signalp” binary is set to the required location:

BEGIN {
    $ENV{SIGNALP} = 'bin/signalp/4.1';
}

TMHMM

Website: http://www.cbs.dtu.dk/services/TMHMM/

There is a download page http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm for academic users; other users are requested to contact CBS Software Package Manager at software@cbs.dtu.dk.

Files required by InterProScan:

  • bin/tmhmm/2.0c/decodeanhmm

  • data/tmhmm/2.0c/TMHMM2.0c.model

Example inteproscan.properties configuration:

tmhmm.signature.library.release=2.0c
binary.tmhmm.path=bin/tmhmm/2.0c/decodeanhmm

tmhmm.model.path=data/tmhmm/2.0c/TMHMM2.0c.model