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The softwares for dot plot analysis perform several tasks. Which one of them is not performed by them?

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The softwares for dot plot analysis perform several tasks. Which one of them is not performed by them?

(a) Gap open penalty

(b) Gap extend penalty

(c) Expectation threshold

(d) Change or mutate residues

I have been asked this question during an interview.

My doubt is from Dot Matrix Sequence Comparison in division Sequence Alignment of Bioinformatics

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Right answer is (d) Change or mutate residues

Easiest explanation: The gap penalties mentioned above are for the determination of score of the aligning sequences. The change in residue barely takes place as there are number of other softwares for that purpose and also the main objective is to find the score of the alignment.

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