Question: (Closed) sequence alignement using python
1
3.7 years ago by
benanfel10
benanfel10 wrote:

hey guys i need your help about something,i need to write a programm using those instructions: input:
1Two protein sequences
2. Algorithm chosen: Needleman-Wunsch or Smith-Waterman (both algorithms must be implemented and it is up to the user to choose the execution of one of the two)
3. Substitution matrix: PAM250 or BLOSUM62
4. Constant penalty: delta

output:
All optimal alignments with the score obtained: In order to obtain the optimal alignments and the corresponding score, the pairwise2 module can be used as follows (local or global alignment): Module Import:

``````From Bio import pairwise2
Call functions:
Alignments = pairwise2.align.globalds (seq1, seq2, matrix, delta, delta)
Alignments = pairwise2.align.localds (seq1, seq2, matrix, delta, delta)
``````
sequence alignment • 1.7k views
modified 3.7 years ago • written 3.7 years ago by benanfel10

Okay, so what's the question?

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i have to get those Results:

``````For seq1 = AGVSILNYA & seq2 = VSILYAKR; Print (alignment) gives:
Global: [('AGVSILNYA--,' - VSIL-YAKR ', -3.0, 0, 11)]
Local: [('AGVSILNYA--,' --VSIL-YAKR ', 21.0, 2, 9)]
``````

Please use `ADD COMMENT` or `ADD REPLY` to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

Hello benanfel!

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