README

Multiple Assembly IntegrAtion with MAIA. 
Last modification: December 15, 2010


REQUIREMENTS

- A Unix operating system
- Matlab 2009b or later (with Bioinformatics toolbox)
- The MUMmer package (nucmer and delta-filter)
- The GAIMC toolbox 


INSTALLATION

1. Add MAIA to your MATLAB Path ( File > Set Path > Add wit subfolders: maia directory )
2. Install MUMmer and make sure nucmer and delta-filter are findable in the unix path
3. Download the gaimc toolbox for Matlab (Graph toolbox)


USAGE

1. Try the CENPK chromosome 9 example, that's in the 'example' folder

	1.1 cd into the ./maia/example folder

	1.2 Run the example by typing: 
	>> maia('assembly_list.txt','./data/ref_genome/chr9_s288c.fa')
	
	1.3 Now the example folder contains the file maia_assembly.fa and one 
	    cytoscape .xgmml per chromosome (only one in this case)
	    
2. Now run maia with yout own data
	>> maia(<tab delimited assembliy list>,  <reference genome>)
	
	The tab delimited assembly list should be in the format:
	AssemblyName1<tab>FastaFileName1<tab>Zscore1
	AssemblyName2<tab>FastaFileName2<tab>Zscore2
	... etc...
	
3. Checkout optional paramters with 
	>> help maia
	



FAQ

1. If your problem is not in the FAQ list, please contact me.


2.  ??? Error using ==> dataread. Buffer overflow (bufsize = 4095) while reading string

    % See 'help textread' to adjust the buffer size parameter
    
    
    Solution: Change line 135 in fastaread.m
    
    ftext = textread(filename,'%s','delimiter','\n');
    
    to for example (depents on your system and requirements)
    
    ftext = textread(filename,'%s','delimiter','\n','bufsize',50000000);


3. Recursion limit reached

    % Dependent on your graph, the recursion limit set by Matlab has to be increased
    set(0,'RecursionLimit',10000)


4. Earlier matlab version are not possible, because I use the tilde (~) to ignore output of 
  functions, which is supported by Matlab since version 2009b 


CONTACT

Jurgen Nijkamp
TU Delft / Pattern Recognition and Bioinformatics
Bioinformatics lab
HB 11.250, Mekelweg 4, 2628 CD Delft
T +31 (0)15 27 83418
E j.f.nijkamp@tudelft.nl


REFERENCE

Jurgen Nijkamp, Wynand Winterbach, Marcel van den Broek, Jean-Marc Daran, Marcel Reinders, and Dick de Ridder 
Integrating genome assemblies with MAIA
Bioinformatics 2010 26: i433-i439.
