Week 3 Feedback

[dtaylo95]

Python script that performs alignment based on user input

2.75/8

Exercise	Points Possible	Grade
Read in inputs	2	1.5
Initialize matrices	1	0.5
Populate matrices	2	0.75
Perform traceback	2	0
Write alignment to file	0.5	0
Print out alignment score and number of gaps in each sequence	0.5	0

DNA alignment file

0/0.5

AA alignment file

0/0.5

README.md with alignment score and number of gaps in each sequence for each alignment

0/1

Total: 2.75/10

Great work so far.

Here's what you need to do for full credit:

• Make sure you fill in the first row and column of your traceback matrix as well
  https://github.com/lws99/qbb2023-answers/blob/4e8f9d73023c78624fade026361e22e7e9838608/week-3/assign_week3.py#L85-L91
• When you're filling in your F-matrix, make sure to use your scoring_matrix, rather than match_score and mismatch_score
  https://github.com/lws99/qbb2023-answers/blob/4e8f9d73023c78624fade026361e22e7e9838608/week-3/assign_week3.py#L106-L115
• Make sure you fill in your traceback matrix as you fill in your F-matrix
• Once the matrices are filled in, do traceback
• From traceback, write the alignments to a file (specified on the command line)
• Print the number of gaps in each sequence and the alignment score, put these in your README.md (for both AA and DNA alignments)
• Upload your two alignment files, and your README.md

[lws99]

I have pushed the updated and corrected assignment! Thank you for the comments!

[dtaylo95]

Nice work! There are two very minor remaining issues:

1. Make sure your while loop end condition is correct. We want to end in the top left, but what happens if row or col reaches 0, but the other does not? https://github.com/lws99/qbb2023-answers/blob/5f7763729567b311e2d5ffc930f0f763db69b4ac/week-3/assign_week3.py#L185
2. No points off, but when you ran the DNA alignment, I think you might have used a -10 gap penalty instead of -300

Current grade: 9.75/10