OPAL download

Ronesh Sharma edited this page Jun 4, 2018 · 47 revisions

#OPAL predictor

OPAL is available as a standalone predictor written and tested in MATLAB and will work on UNIX systems see terms and conditions for use. To download OPAL as MATLAB package, please click here.

OPAL 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 OPAL on UNIX system

  • Unpack: tar -zxvf OPAL.tar.gz
  • cd OPAL

#Installing the support packages:

  • OPAL requires installation of SPIDER2 package, BLAST and its databases, MoRFchibi package, MATLAB/OCTAVE, GAWK and other basic compilers:

1. Installing SPIDER2 package

  1. SPIDER2 package can be downloaded from "http://sparks-lab.org/pmwiki/download/index.php?Download=yueyang/SPIDER2-hse_local.tgz"

  2. unpack: tar xzvf SPIDER2-hse_local.tgz

  3. Install Blast: SPIDER2 requires BLAST+ software package to be installed with NR database. BLAST+ can be downloaded from NCBI: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download. Alternatively, BLAST+ can be installed on Ubuntu system using command line: sudo apt-get install ncbi-blast+

NR dataset: you can download them from "ftp://ftp.ncbi.nlm.nih.gov/blast/db/"

Note: Please in file "/SPIDER2_local/misc/run_local.sh" change the blastpgp & NR database path to correct addresses.

e.g. blastpgp=/usr/bin/psiblast and NR=/home/pub/blast/NR/nr

2. Installing MoRFchibi package

  1. MoRFchibi can be downloaded from "http://www.chibi.ubc.ca/wp-content/uploads/2016/03/MCS1.03.tar.gz"
  2. Unpack:
  • tar -zxvf MCS1.03.tar.gz
  • cd MCS1.03
  • Compile: g++ -O3 source/mc.c source/*.cpp -o mc

3. Installing MATLAB and LibSVM tool box

  1. 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.

  2. OPAL 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.

Note: LibSVM MATLAB/OCATVE binaries are required to be built using make file and its path to be included in “properties.txt’ file in OPAL directory.

4. Installing other compilers using command line:

sudo apt-get install gawk

sudo apt-get install python

sudo pip install scipy

sudo apt-get install python-scipy

sudo pip install -I numpy==1.11.1

Using OPAL

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

  • Path to spider2_local misc dir must be adjusted
  • Path to LibSVM MATLAB binaries must be adjusted
  • Path to PROMIS dir must be adjusted
  • Path to MoRFchibi MCS1.03 dir must be adjusted

To run OPAL predictor:

  • The query sequence in fasta format should be kept in OPAL directory as input.fasta
  • if pssm file is available for query sequence, then should be kept in OPAL directory as input.pssm

For demo: input sequence and pssm files are available in OPAL directory for protein sequence of length 207

run_OPAL.m file can be used to predict MoRF scores

  • e.g. run_OPAL('sequence'); #input: query sequence
  • or e.g. run_OPAL('sequence','pssm'); #input: query sequence and pssm file if available (if pssm file available, it will not be computed)

The input query file will be processed and results will be saved as scores_OPAL.txt file

Note: To call run_OPAL function, Demo.m file is given. If you are using OCTAVE graphical user interface you can open Demo.m and simulate. This will run run_OPAL function with default input as sequence only. If you are calling from command line, you can type 'sudo octave --eval Demo'.

Alternatively, PROMIS predictor can be also used similar way:

  • e.g. run_PROMIS('sequence'); #input: query sequence
  • or e.g. run_PROMIS('sequence','pssm'); #input: query sequence and pssm file if available

The input query file will be processed and results will be saved as scores_PROMIS.txt file

Demo.m file is given as a demo to run predictors OPAL and PROMIS using either MATLAB or OCTAVE.

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