• Email your script and output file to bioinfo.rpi@gmail.com. The subject of the email should be assign1-rcsid.

• 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.

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

• 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

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

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

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

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

• 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

Sequence Alignment

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.

Part 1

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

• Document (word/pdf/txt) that includes your answers: local alignment output , using linear gap penalty of -4, and a gap opening and extension penalty of -5 and -2, respectively
• Your program files, named as LocalAlignmentLinear.XX and LocalAlignmentAffine.XX, where XX is either "py" or "r". Do not hard code path names. Assume that the two sequences and BLOSUM62 matrix are in the local dir.

In this assignment you will write a program to perform a local alignment of two protein sequences, using the BLOSUM62 scoring matrix, and using affine gap penalties (-5 for gap opening, and -2 for gap extension). You must write your own program for the alignment, but you can use library functions (from biopython) to read the sequences and substitution matrices.

Due Date: Friday, Feb 10, 11:59:59pm (i.e., before midnight)

What to turn in

• Document (word/pdf/txt) that includes your answers: 1) local alignment output.
• Your program file as a single file called LocalAlignment.XX. XX is either "py" or "r". Do not hard code path names. Assume that the two sequences and BLOSUM62 matrix are in the local dir.

Best Local Alignment: score= 24.0 len= 10

In this assignment you will write a program to perform a local alignment of two protein sequences, using the BLOSUM62 scoring matrix, and using affine gap penalties (-5 for gap opening, and -2 for gap extension). You must write your own program for the alignment, but you can use library functions (from bioperl or biopython) to read the sequences and substitution matrices.

In this assignment you will write a program to perform a local alignment of two protein sequences, using the BLOSUM62 scoring matrix, and using affine gap penalties (-5 for gap opening, and -2 for gap extension). You must write your own program for the alignment, but you can use library functions (from or ) to read the sequences and substitution matrices.

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= 26.0 len= 10
seq1 pos= 0 7 seq2 pos= 0 10

HPQ---PATY
HPQNQSPAAH

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

Best Local Alignment:  score= 27.0 len= 10
seq1 pos= 0 7 seq2 pos= 0 10

HP--Q-PATY
HPQNQSPAAH

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

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

HPQ
HPQ

Submit an email with the following:

• Document (word/pdf) that includes your answers: 1) local alignment output, and 2) the gene names/functions.

Sequence Alignment & Function

Due Date: Feb 14, 11:59:59pm

Step 1: Local Alignment

In this assignment you will write a program to perform a local alignment of two protein sequences, using the BLOSUM62 scoring matrix, and using affine gap penalties (-5 for gap opening, and -2 for gap extension). You must write your own program for the alignment, but you can use library functions 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

Step 2: BLAST

After you find the best local alignment, copy and paste the aligned region into the NCBI protein blast server to find out the gene that produces these proteins in Humans (Homo Sapiens) and Fruit Fly (Drosophila Melanogaster). You can do two separate BLAST searches, one for Human and one for Fruit Fly. Describe the name/function of this gene in both organisms.

Step 3: What to turn in

• Create a document (word/pdf) that includes your answers: 1) local alignment output, and 2) the gene names/functions.
• Your program file as a single file called LocalAlignment.XX. XX is either "pl", "py" or "r". Do not hard code path names. Assume that the two sequences and BLOSUM62 matrix are in the local dir.

Late Policy

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