[EMBOSS] Stretcher & custom scoring matrix

Ryan Golhar golharam at umdnj.edu
Mon Dec 5 22:40:48 UTC 2005

I'm using stretcher with a custom scoring matrix I created.  It works
for 99% of my sequence.  Occassionally, I get the waring:

Warning: stretcher CheckScore failed

I'm using a gapopen penalty of 160000 and gapextend of 40000.  This is
because I need to normalize my matrix from floating point to integer.  I
suspect this has something to do with it.  

What does this error mean?


More information about the EMBOSS mailing list