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Ronesh Sharma edited this page Aug 22, 2018 · 42 revisions

#MoRFpred-plus predictor

MoRFpred-plus is available as a standalone predictor written and tested in C code and MATLAB, see terms and conditions for use. To download MoRFpred-plus as a MATLAB package please click here.

MoRFpred-plus is optionally available as a OCTAVE package (open-source package) please click here to download. In this package OCTAVE is used instead of MATLAB.

#Installation To install MoRFpred-plus on UNIX system

  • Unpack: tar -zxvf MPP.tar.gz (or tar -zxvf MPP_octave.tar.gz if using OCTAVE package)
  • cd MPP
  • Compile: make

#Installing the support packages:

MoRFpred-plus requires installation of HHblits and its databases, MATLAB/OCTAVE, GAWK and other basic compilers:

1.Installing HHblits (version 2.0.16 or later) and its databases

HHblits can be installed on Ubuntu system using command line: sudo apt-get install hhsuite

To run MoRFpred-plus, HHblits software package requires nr20_latest database to be installed.

nr20_latest database is available at the download page : ftp://toolkit.genzentrum.lmu.de/HH-suite/databases/

Alternatively, uniprot20 database can be used, it is available at download page: http://wwwuser.gwdg.de/%7Ecompbiol/data/hhsuite/databases/hhsuite_dbs/

Note: Extract the tar file and in “properties.txt’ file in MPP directory, line that identifies the directory path to HHblits database needs to be appropriately edited.

2.Installing MATLAB (version 2015a or later)/OCATVE (version 4.0 or later) and LibSVM tool box (version 3.21 or later)

If using MATLAB package, download and install MATLAB from Mathworks OR if using OCTAVE package, install OCTAVE by command line: sudo apt-get install octave

MoRFpred-plus uses LibSVM tool (Chang and lin 2011) for classification task, LibSVM package is available at the download page: http://www.csie.ntu.edu.tw/~cjlin.

LibSVM MATLAB/OCTAVE binaries are required to be built using make file and its path to be included in “properties.txt’ file in MPP directory.

3.Installing other compilers

MoRFpred-plus require gawk to be installed. Gawk can be installed on Ubuntu system using command line: sudo apt-get install gawk

##Using MoRFpred-plus

To use MoRFpred-plus, first all the required compilers and packages mention above must be installed. Secondly, “properties.txt’ file in MPP directory must be edited as follows:

  1.  Path to MATLAB/octave must be adjusted
  2. Path to combine.m must be adjusted
  3. Path to LibSVM MATLAB/octave binaries must be adjusted
  4. Path to query sequence txt file must be adjusted
  5. Path to HHblits database (nr20_latest) must be adjusted
  6. Path to save hmmprofile txt file must be adjusted

###To run:

type sudo ./mp

  • The input file demo_query_seq.txt will be processed and results will be saved to scores.txt file
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