CAP 5937 ST: Bioinformatics
Assignment-2 
Due Date: 09/27/2004
 
 
Write a program to enumerate the best global alignment between two amino acid sequences. 
The program should take two input amino acid sequences in FASTA format, and the alignment 
matrix in the standard format as in the following BLOSUM and PAM matrices. Assume a uniform 
gap penalty, given by the * column in the corresponding alignment matrix.
 
Deliverables:




1. Source code (C, C++, Java or Perl)
2. Instructions for compiling the source
3. Sample output, for the pair wise alignment between the following two amino acid sequences 
using the BLOSUM62 alignment matrix. 
 
 
Sequences:
 
>gi|2500564|sp|P70709|ECP_RAT Eosinophil cationic protein precursor (ECP) (Ribonuclease 3) (RNase 3)
MGLKLLESRLCLLLSLGLVLMLASCQPPTPSQWFEIQHIYNRAYPRCNDAMRHRNRFTGHCKDINTFLHT
SFASVVGVCGNRNIPCGNRTYRNCHNSRYRVSITFCNLTTPARIYTQCRYQTTRSRKFYTVGCDPRTPRD

SPMYPVVPVHLDRIF

>gi|119124|sp|P12724|ECP_HUMAN Eosinophil cationic protein precursor (ECP) (Ribonuclease 3) (RNase 3)
MVPKLFTSQICLLLLLGLMGVEGSLHARPPQFTRAQWFAIQHISLNPPRCTIAMRAINNYRWRCKNQNTF
LRTTFANVVNVCGNQSIRCPHNRTLNNCHRSRFRVPLLHCDLINPGAQNISNCRYADRPGRRFYVVACDN
RDPRDSPRYPVVPVHLDTTI

Matrices:

BLOSUM45

BLOSUM62

BLOSUM80

PAM30

PAM70