[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
-datafile:
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
conversion".
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
before?
Ryan
More information about the EMBOSS
mailing list