Question: (Closed) sequence alignement using python
1
gravatar for benanfel
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
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by benanfel10

Okay, so what's the question?

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:

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ADD REPLYlink written 3.7 years ago by WouterDeCoster45k

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)]
ADD REPLYlink modified 3.7 years ago by WouterDeCoster45k • written 3.7 years ago by benanfel10

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:

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ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by WouterDeCoster45k

Hello benanfel!

We believe that this post does not fit the main topic of this site.

Not a question, please don't just post your homework, but make an effort.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 3.7 years ago by Michael Dondrup48k
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