Programming Assignment 2	Due: Mar 18, Wednesday
Points: 30

Assignment on Local Alignment using Dynamic Programming. 

Groups:
Sally, Luis, Stephen,
Greg, Richie, Ray
Griffin, Azhar, Vaibhav
Srividya, Nathan, Vikas


Find the best local alignment(s) in the folowing pair of proteins. Use BLOSSUM-xx matrix (as in the class slides from the Text).

Two proteins I have chosen are below. BLAST the protein 1 on UniProt database that should find the second sequence.  Compare your local alignment(s) with the  BLAST result.

Protein 1:
SOURCE: http://www.uniprot.org/uniprot/Q3B833.fasta

>tr|Q3B833|Q3B833_HUMAN IGF1R protein (Fragment) OS=Homo sapiens GN=IGF1R PE=2 SV=1
GQEGQQGCVQCSRRTLVCGKPLQAAHEASWPCAPSRFGPPPVCLGCRFELMRMCWQYNPK
MRPSFLEIISSIKEEMEPGFREVSFYYSEENKLPEPEELDLEPENMESVPLDPSASSSSL
PLPDRHSGHKAENGPGPGVLVLRASFDERQPYAHMNGGRKNERALPLPQSSTC

Protein 2:
SOURCE: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=VNAHJCXA01R&log%24=prottop&blast_rank=1&list_uids=78070529
LOCUS       AAI07090                 173 aa            linear   PRI 11-APR-2007
DEFINITION  IGF1R protein [Homo sapiens].
ACCESSION   AAI07090
VERSION     AAI07090.1  GI:78070529
DBSOURCE    accession BC107089.1
KEYWORDS    .
SOURCE      Homo sapiens (human)

gqegqqgcvq csrrtlvcgk plqaaheasw pcapsrfgpp pvclgcrfel mrmcwqynpk mrpsfleiis sikeemepgf revsfyysee nklpepeeld lepenmesvp ldpsassssl plpdrhsghk aengpgpgvl vlrasfderq pyahmnggrk neralplpqs stc


Submission/per group: Hard copy of well-commented code with sample run on the above example, and the run time.