Needleman and Wunsch Algorithm

Question

[anasjamshed]

I have 2 Sequences:

• Seq1: CGATCAT
• Seq2: ATCA

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

I aligned them through Needlman and Wunsch:

and get this answer:

Can anyone verify this answer?

[Michael]

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.

[anasjamshed]

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

Answer 1

[Mensur Dlakic]

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?