Assign 1

* 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 '''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.

* < 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 you method.

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

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

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

* 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

! Sequence Alignment & Function

!!!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 (from [[http://www.biopython.org|biopython]]) to read the sequences and substitution matrices.

* Document (word/pdf/txt) that includes your answers: 1) local alignment output.
* Your program file as a %red%'''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.

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 [[http://www.bioperl.org|bioperl]] or [[http://www.biopython.org|biopython]]) to read the sequences and substitution matrices.

%red% '''Due Date''': Feb 14, 11:59:59pm%%

!!!Step 2: BLAST

After you find the best local alignment, copy and paste the aligned region into the [[http://blast.ncbi.nlm.nih.gov/Blast.cgi | 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

* Document (word/pdf) that includes your answers: 1) local alignment output, and 2) the gene names/functions.
* Your program file as a %red%'''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.

Best Local Alignment: score= 26.0 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 [[www.bioperl.org|bioperl]] or [[www.biopython.org|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 to read the sequences and substitution matrices.

* Create a document (word/pdf) that includes your answers: 1) local alignment output, and 2) the gene names/functions.