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Even if many pseudocounts are added in comparison to real sequence counts, the amino acid frequencies will not have any effect or influence.

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Even if many pseudocounts are added in comparison to real sequence counts, the amino acid frequencies will not have any effect or influence.

(a) True

(b) False

I got this question in an online interview.

My enquiry is from Position in division Multiple Sequence Alignment of Bioinformatics

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Correct choice is (b) False

Explanation: Knowing how many counts to add is a difficult but fortunately solvable problem. On the one hand, if too many pseudocounts are added in comparison to real sequence counts, the pseudocounts will become the dominant influence in the amino acid frequencies and searches using the motif will not work. On the other hand, if there are relatively few real counts, many amino acid variations may not be present because of the small sample of sequences.

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