Second Perl Problems:

Problem 2: Take the data set from problem 1, and now write a Perl
script (short program) which locates all the open reading frames
(ORF's) and reports their locations and lengths. Have your program
tell you which ORF is the longest. In preparation for future problems,
have the program save your ORF's to a separate file, where they are
labeled (numbered) and stored.

Problem 3: Write a program which takes the ORF's of problem 2, and
computes the codon frequencies within those ORF's. This might suggest
to you writing a subroutine you could call up so you don't have to
write a long if_elsif... loop which describes all 64 codons more than
once.

Problem 4: Go to GenBank and pull down a FastA file of any gene at
least 1500 nt long. Analyze this for frequencies of the different
glycine codons (there are several). "Codon usage bias" is a standard
way to look for a signature of genomic sequence.