Assign 1

Sequence Alignment

Due Date: Monday, Feb 11, 11:59:59pm (i.e., before midnight)

Local Alignment

In this assignment you will write a program to perform a local alignment of two protein sequences, using the BLOSUM62 scoring matrix. You must write your own program for the alignment, but you can use library functions (from biopython) to read the sequences and substitution matrices.

Here are the two sequences you have to align in FASTA format: seq1.txt, and seq2.txt. The BLOSUM62 data is here: BLOSUM62.txt

Part 1

Write the basic method for linear gap penalty. Make the penalty an input parameter for your method.

Part 2

Extend the code to handle affine gap penalties, i.e., a separate gap opening, and gap extension penalty. Both of these should be input parameters.

What to turn in

  • Document (word/pdf/txt) that includes your answers: local alignment output, using linear gap penalty of -3, and a gap opening and extension penalty of -5 and -2, respectively
  • Your program files, named as assign1-rcsid-linear.XX and assign1-rcsid-affine.XX, where XX is either "py" or "r", and rcsid is your RCS id. Do not hard code path names. Assume that the two sequences and BLOSUM62 matrix are in the local dir.
  • Email your script and output file to bioinfo.rpi@gmail.com. The subject of the email should be assign1-rcsid.

Sample Output

To check your code you may use these two short sequences: 

>s1
HPQPATY

>s2
HPQNQSPAAH

With gap opening penalty of -5 and gap extension penalty of -2, your output should match: 

Best Local Alignment:  score= 24.0 len= 10
seq1 pos= 0 6 seq2 pos= 0 9

HPQ---PATY
HPQNQSPAAH

With gap opening penalty of -2 and gap extension penalty of -2 (i.e., a linear gap penalty of -2), your output should match: 

Best Local Alignment:  score= 27.0 len= 10
seq1 pos= 0 6 seq2 pos= 0 9

HP--Q-PATY
HPQNQSPAAH

With gap opening penalty of -5 and gap extension penalty of -5 (i.e., a linear gap penalty of -5), your output should match: 

Best Local Alignment:  score= 20.0 len= 3
seq1 pos= 0 2 seq2 pos= 0 2

HPQ
HPQ

Late Policy

  • < 9 hours late: 10% penalty, 9-24 hours late: 25% penalty, 24-48 hours late: 50% penalty, > 48 hours: 100% penalty