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#Arun Ramani & Edward Marcotte
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#MATRIX README
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#Last Modified 12/17/04
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#Modifications: NONE (all original files)
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This directory contains the following files.
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PROGRAMS:

format_phylip_mat_for_sa_wnames.pl 

use this to convert the dst output from your alignment program to 
the format accepted by simulated annealing program. 
the example of the format is the
example_of_sa.sa file.

the .sa extension is not necessary, it can be anything you want....this
is just to let me know that it is formatted for sim anneal (sa).


randomizematrix_total.pl

use this to convert one of the files into a random format, so that the 1-1 
correspondence is not maintained anymore. 


simanneal_wnames.pl

use the randomized file (say of the sensor) and the original regulator 
with a temperature term. set the temperature of annealing such that 
the initial acceptance of rmsd change is > 0.8 at least. this is an arbitary
assignment and you can increase it or decrease it if you feel so. 


MISC INFORMATION:

we use a wrapper program to carry out these steps iteratively (100 times) and 
remember the results from each of the runs. we also do the final matrix voting 
to establish the 'correct' assignments.
it would be trivial to write a wrapper. if i have too many requests for the wrapper, i 
will add it to the website.


#==========================================================
#send comments/questions to arun at icmb dot utexas dot edu
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