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-- %TEACHINGWEB%.TahouraSamad - 13 Nov 2011
Homework 6:

Hi Mohammad, I would like this to be graded with grading scheme 1.
I have included my program as NWfinal.pl, as well as a Blosum 62, Blosum 50 and DNA similarity matrix I used to test my code, and a couple of the sample sequence files I used to check my code.

I have tested my code fairly extensively and it should/has been able to:
1. Correctly read in the similarity matrix.
2. Correctly read in the strings.
3. I completed the basic error handling, as described by Professor Holmes in the body of the assignment, and completed each of the bullets innumerated by Mohammad on the linked page Pairwise alignment error checking.
3. Completes running in under a minute for strings of length 100. (Can run strings much longer than this in under a minute).
4. Correctly generates a score matrix and prints it to a file called scorematrix.txt. (I verified some of the shorter ones by hand)
5. Correctly generates alignment based on back tracking.

I have not run across any errors but if there are any, I would guess that they would be as a result of error handling, as I first got the core of my program (ability to read in perfect files, similarity matrices, generate scoring matrix, generate alignment etc) first, and then added in all the error handling at the end.

thanks!

I	Attachment	Action	Size	Date	Who
txt	Dna.txt	manage	0.1 K	2011-11-13 - 05:56	TahouraSamad
txt	NWfinal.pl.txt	manage	6.9 K	2011-11-13 - 05:54	TahouraSamad
txt	blosum.txt	manage	1.4 K	2011-11-13 - 05:55	TahouraSamad
txt	blosum50.txt	manage	1.5 K	2011-11-13 - 05:55	TahouraSamad
txt	protein2.txt	manage	0.5 K	2011-11-13 - 05:58	TahouraSamad
txt	similaritymatrix.txt	manage	0.1 K	2011-11-13 - 05:56	TahouraSamad
txt	yas12.txt	manage	1.0 K	2011-11-13 - 05:59	TahouraSamad

Parents: TWikiUsers > TahouraSamad