Determine the cross-validation accuracy of Needleman-Wunsch with and
without affine gaps and with and without BLOSUM62 matrix for the 
training.txt datasets in PREFAB. 

Use match cost of +5 and mismatch cost of -4 when testing without BLOSUM62 
and otherwise use the BLOSUM62 matrix.

Select the best gap open from the set 

@go = (-16, -14, -12, -10, -8, -6, -4, -2);

and the best gap extension from the set

@ge = (-2, -1, -.5, -.1);

## Assignment details ##

Submit your Perl scripts by copying them into the directory
/afs/cad/courses/bnfo/f18/bnfo/601/001/<ucid>.
For example if your ucid is abc12 then copy your Perl scripts into
/afs/cad/courses/bnfo/f18/bnfo/601/001/abc12.
         
Make sure your affine alignment script and the alignment accuracy scripts are 
also there.

Also submit a file that shows the table below and your errors.
The numbers below are the mean training error for all methods 
except affine gaps with BLOSUM62 matrix.

		Non-affine	Affine
Match/mismatch	55.8 (-16)	51.2 (-16,-2)
BLOSUM62	49.2 (-8)	42.5 (-16,-1)