Thursday, October 17, 2013

Installation of secretome in your server

We are also working on probiotic bacteria and analyzed few secretory proteins from MALDI. As it turns out, some of the secretory proteins are predicted to signalp positive and some are not. Intrigued, we did a secretome analysis on those and found all the secretory proteins to be either signalP positive or secretome positive. We got a copy of secretome from . Untarred and got the package. However, it has a large number of dependencies and they are:

1. ProP 1.0
3. seg
4. TMHMM 1.0
5. SignalP 3.0

ProP 1.0
Prop predicts arginine and lysine cleavage sites using ensemble Neural Network. By default it does a Furin specific prediction. It also does a proprotein convertase prediction and has been integrated into signalp.
For installation of this package, you have to open the 'prop' executable file and start editing the paths in the following section:

else if ( $SYSTEM == "Linux" ) then # typical Linux
setenv AWK /usr/bin/gawk setenv ECHO "/bin/echo -e" setenv GNUPLOT /usr/local/bin/gnuplot # /usr/local/bin/gnuplot-3.7 #setenv PPM2GIF /usr/bin/ppmtogif # I could not find a ppmtogif package in my installation so I did the following:
setenv PPM2GIF /usr/bin/ppm2tiff setenv SIGNALP /usr/cbs/bio/bin/signalp

set appropriate path after checking the path of the above mentioned programs.

Now set PROPHOME correctly in prop script.

setenv PROPHOME /usr/adadata/prop-1.0c

Then just test by running ./prop and see if it runs fine.


I obtained a copy by emailing: Yuki Saito <> secretary to prof Prof. Kenta Nakai
This is a very useful program used for predicting sub-cellular localization of a protein and is a perl script. All that you need to do it in the sha bang line set the correct path for perl!

Test it by running ./psort . If it runs fine, then installation is OK.


It comes with the blast distribution.

SignalP and TMHMM : 

Can be obtained from the same ( place and can be installed.

Once all the installations are done check if all of these programs are working. In case, all are running fine, then go back to secretomep script and set the correct paths to all the existing programs:

Here is a template of my changes:

else if ( `uname` == "Linux" ) then

   setenv ECHO  "/bin/echo -e"
   setenv AWK   /usr/bin/gawk
   setenv PERL  /usr/bin/perl

   set prop     = /usr/adadata/prop-1.0c/prop
   set psort    = /usr/adadata/psort/psort
   set seg      = /usr/adadata/ncbi-blast-2.2.28+/bin/segmasker
   set tmhmm    = /usr/adadata/tmhmm-2.0c/bin/tmhmm
   set signalp  = /usr/adadata/signalp-4.1/signalp


Once done just run ./secretomep in silent mode and see if it runs fine...

[our installation was successful]


  1. mam am really glad to c this made it, ur the one to solve all our issues always we come mam this is not working, this is not running, with the patience u hear all our issues and solve it hatsoff soon we will learn some techniques from u mam

    1. Hi madhu r u from bioinformatics, what is ur area of work, nice to c a peoples working in bioinformatics