README

Project 3
Rohit Gopal

CMSC423 0101


The files included for this submission are: 
proj3_rgopal.pl  


proj3_rgopal.pl 	This is my submission for the project.  It uses
			BioPerl for reading in the files and then performs
			a local alignment on the first sequence in each
			file passed in as arguments. 

To Run the Project:

./proj3_rgopal.pl <fasta file> <fasta file> <HOXD2 FILE> <gap_open> <gap_extend>

This project reads in the HOXD2 Format.


The output is to stdout, and assumes that the naming schema is 

seq1_id start_index <basepairs> end_index
                    <alignment> 
seq2_id start_index <basepairs> end_index

where seq1_id is the id for the first sequence in the first fasta file and
seq2_id is the corresponding id for the second sequence.  The output should only
be up to 80 characters in width.