[EMBOSS] Custom Scoring Matrix

Ryan Golhar golharam at umdnj.edu
Fri Dec 2 20:49:01 UTC 2005

I've created a custom scoring matrix of log-odds probabilities for
comparing certain types of sequences.

I'm not trying to use stretcher to compare two sequences using my
matrix.  I'm passing in the matrix as an option to stretcher using

stretcher -asequence a.fasta -bsequence b.fasta -datafile ./matrix.mat 

I get an error "EMBOSS An error in ajarr.c at line 1752: Bad integer

My matrix looks something like this:

        A       C       G       T
A       1.1619  -0.9808 -0.7169 -1.2463
C       -1.1165 1.54077 -0.8689 -0.8288
G       -0.7911 -0.8621 1.5170  -1.1425
T       -1.2419 -0.7391 -1.0441 1.0995

I take it from the error, strether requires integers.  Is that true, or
is the error generic?  If it requires integers, then I will need to find
a way to normalize this matrix to integers.  Has anyone done this


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