BINF 634
Programming Assignment 2

Due: Monday,  October 12, 2009, 7pm

Like many viruses, Hepatitus B Virus (HBV) has a circular genome,
meaning that coding regions can "wrap around" the virus.  In this
assignment, you will write a Perl program to find all the possible
protein coding regions in a circular genome.

Specifications:  Write a Perl program called cds.pl that takes one
command line argument, the name of a FASTA file.  You may assume that
the FASTA file contains a single sequence.  Run your program as follows:

% cds.pl filename

Input: A FASTA format file containing the genomic DNA.

Output: First print out the original DNA sequence, including the header
line.  Print the DNA sequence using 60 characters per line.

Then print to the screen a list of possible coding regions, or CDS.  In
GenBank a CDS is a region of nucleotides that corresponds with the
sequence of amino acids in a protein.  Output format is shown below,
based on the format of a GenBank record. (For HBV, see
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=21326584 ).
The first line gives the location of the CDS in genomic coordinates (the
first base is labeled 1).  The second line begins with "/translation=",
followed by the protein sequence. All lines contain a maximum of 58
characters.  Print a blank line between each CDS.  The location of the
CDS includes start and stop codons, but the stop codon is not printed.

CDS 155..835
/translation="MESTTSGFLGPLLVLQAGFFLLTRILTIPQSLDSWWTSLNFLGG
APTCPGQNSQSPTSNHSPTSCPPTCPGYRWMCLRRFIIFLFILLLCLIFLLVLLDYQG
MLPVCPLLPGTSTTSTGPCRTCTIPAQGTSMFPSCCCTKPSDGNCTCIPIPSSWAFAR
FLWEWASVRFSWLSLLVPFVQWFVGLSPTVWLSAIWMMWYWGPSLYNILSPFLPLLPI
FFCLWVYI"

If a coding region wraps around the end of the sequence, the first line
indicates the sections that make up the CDS, as follows:

CDS join(2848..3215,1..835)
/translation="MGGWSSKPRQGMGTNLSVPNPLGFFPDHQLDPAFGANSNNPDWD
FNPNKDHWPEANQVGAGAFGPGFTPPHGGLLGWSPQAQGILTTLPAAPPPASTNRQSG
RQPTPISPPLRDSHPQAMQWNSTTFHQALLDPRVRGLYFPAGGSSSGTVNPVPTTASP
ISSIFSRTGDPAPNMESTTSGFLGPLLVLQAGFFLLTRILTIPQSLDSWWTSLNFLGG
APTCPGQNSQSPTSNHSPTSCPPTCPGYRWMCLRRFIIFLFILLLCLIFLLVLLDYQG
MLPVCPLLPGTSTTSTGPCRTCTIPAQGTSMFPSCCCTKPSDGNCTCIPIPSSWAFAR
FLWEWASVRFSWLSLLVPFVQWFVGLSPTVWLSAIWMMWYWGPSLYNILSPFLPLLPI
FFCLWVYI"

The program should print out each CDS in all three forward reading
frames.  In order to match the output in the sample, make sure that you
print out all CDS for reading frame 1 first, followed by the CDS from
readings frames 2 and 3.

Rules for finding possible coding regions:
1. Coding regions begin with a start codon ATG, which translates to M
  (Methionine).
2. Coding regions end with a stop codon (TAA, TAG or TGA), and
   no other stop codons occur between the start codon and the stop codon
   at the end of the coding region.
3. Coding regions may contain more than one Methionine.
4. Coding regions may overlap.  For example, the DNA sequence ATG TTA
ATG CCT TAG contains two coding regions that translate as MLMP_ and MP_
(where "_" indicates the STOP codon.)  In this case, you would print
them both.
5. Include the first Methionine ("M") in the CDS, but do not print the
  STOP codon ("_").

Your program will print out more CDS regions than appear in the GenBank
record, because not all possible coding regions actually code for
proteins.

Sample input and output is available on the course web site, created as follows:

% cds.pl hbv.fsa > cds.out

I may test your program on other input files, so don't hard code the
answers for this example.

Due Date: Submit the assignment via email to me by 7pm on October 12, 2009.
Late assignments will not be accepted.

Use of other code: You may freely use any code discussed in class or in
the text book, including the functions in the module
BeginPerlBioinfo.pm, described in Ch. 8.  Use of any code from any other
source is strictly prohibited.