Write a Perl script to align two DNA sequences in FASTA format
using a hidden Markov model. Follow the algorithm sketched out in
the slides and that we implemented in class. You may start with the
initialization code provided on the class website.

After you have implemented the HMM write a Perl script to perform 
cross-validation on the two parameters delta and eta from the set

@delta = (.1, .15, .2, .25, .3, .35, .4, .45, .5);
@eta = (.2, .25, .3, .35, .4, .45, .5, .55, .6);

Your cross-validation script should print out the delta-eta
pairs sorted by their cross-validation error.

The due date is 2:30pm Nov 12th 2018.

Submit your assignment by copying it into the directory
/afs/cad/courses/bnfo/f18/bnfo/601/101/<ucid>. 
For example if your ucid is abc12 then copy your Perl script into
/afs/cad/courses/bnfo/f18/bnfo/601/101/abc12.