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