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Needleman and Wunsch Algorithm

I have 2 Sequences:

  • Seq1: CGATCAT
  • Seq2: ATCA

and match = 0 , mismatch =1 and gap = 2

I aligned them through Needlman and Wunsch:

needleman

and get this answer:

answer

Can anyone verify this answer?

alignment needleman-wunsch
• 1,652 views • link
updated by Ram Ram • written by anasjamshed anasjamshed

I think your answer is "correct" given this odd scoring scheme. As Mensur already noticed, this scoring scheme will not produce any alignments in the sense we are used to, instead concatenates the sequences and fill with as many gaps as possible. Gap and mismatch scores are also called "penalties" and should yield a negative score, so your scoring scheme should really look like this: match = 1, mismatch = -1, gap = -2. Note the resulting optimal score for your example will be negative.

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written by Michael Dondrup Michael Dondrup

Instead of using the max value in formula can we use min in case if penalities are greater than match?

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written by anasjamshed anasjamshed

1 answer

We are not here to help with homework, but I will point you to this paper:

https://www.nature.com/articles/nbt0704-909

Out of curiosity, what is the purpose of a scoring scheme where a gap is scored higher than a mismatch, and a mismatch is scored higher than a match?

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

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