Author: Gary Bader - Jan.2003

Please see the following paper for more information:

Bader GD, Hogue CW.

An automated method for finding molecular complexes in large protein interaction networks.
BMC Bioinformatics. 2003 Jan 13;4(1):2.
http://www.biomedcentral.com/1471-2105/4/2

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12525261&dopt=Abstract

Installation instructions:
1. Unpack files into a directory.
2. For Windows, edit the yilib\yilib.ini file appropriately and put the .ini file in your windows directory. (e.g. C:\WINNT)
   For UNIX, edit the .yilibrc file appropriately and place the file in your home directory.
   MCODE requires these configuration files for the Yeast database (YILIB) that is included.

Running instructions:
MCODE arguments:

  -r  Root name of output files. [String]
  -i  Input gene name pair list (interactions). Tab-delimited list. [File In]
  -g  T if input is a list of GI's. [T/F]  Optional
    default = F
  -d  Depth from source node to limit complex finding. [Integer]  Optional
    default = 100
  -c  Degree cut-off for node scoring. [Integer]  Optional
    default = 0
  -t  Node score percentage threshold for core complex expansion. [Real]  Optional
    default = 0.2
    range from 0.0 to 1.0
  -h  Give complexes a haircut (remove singly connected nodes). [T/F]  Optional
    default = T
  -f  Fluff complexes (expand core complex one neighbour shell outwards according to -e flag). [T/F]  Optional
    default = F
  -e  Neighbour density percentage threshold for complex fluffing. [Real]  Optional
    default = 0.1
    range from 0.0 to 1.0
  -s  Directed mode. Try to find a complex around a given protein in the network (stops after finding one complex). [String]  Optional
  -p  Preprocess network for directed mode (If F, will allow complex to branch out to denser complexes). [T/F]  Optional
    default = T
  -a  Export annotation file for each complex. [T/F]  Optional
    default = T
  -l  Name of log file. If name is provided, a log file will be generated. [File Out]  Optional
  -y  Colour networks option. 1=YPD Function, 2=YPD Localization, 3=YPD Role, 4=GO Localization, 5=GO Process, 10=MCD Score, 11=Nothing [Integer]  Optional
    default = 10
  -o  Output CASTA formatted file of complexes [T/F]  Optional
    default = F

----------------------------------------------------------------------------------------
An example protein interaction list is provided to try MCODE called y2h-nr.txt
This file contains almost all yeast protein interactions reported until Aug.2002.

Output files ending in -annot.txt can be loaded into Excel for easy viewing of annotation of proteins in the complex.

Output files ending in .net can be loaded into Pajek (see instructions in "Basic Pajek Instructions.doc")

If -y is selected with an appropriate option, a file ending in ColourMap.txt will be output with each complex to tell
you which Pajek node colour represents which biological protein function.

----------------------------------------------------------------------------------------
If you have questions about this software, please e-mail:
gary.bader@utoronto.ca or hogue@mshri.on.ca

Current supported platforms are Windows and Linux.
If you would like other platforms supported, please e-mail:
hogue@mshri.on.ca or gary.bader@utoronto.ca

<End of Readme>

