sequence alignement using python

Question: (Closed) sequence alignement using python

3.7 years ago by

benanfel • 10 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

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modified 3.7 years ago • written 3.7 years ago by benanfel • 10

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 REPLY • link written 3.7 years ago by WouterDeCoster ♦ 45k

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 REPLY • link modified 3.7 years ago by WouterDeCoster ♦ 45k • written 3.7 years ago by benanfel • 10

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.

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ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by WouterDeCoster ♦ 45k

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 REPLY • link written 3.7 years ago by Michael Dondrup ♦ 48k

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