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The second step in the Genetic Algorithm comprises of scoring of the 100 initial MSAs by the sum of pairs method.

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The second step in the Genetic Algorithm comprises of scoring of the 100 initial MSAs by the sum of pairs method.

(a) True

(b) False

I have been asked this question in a national level competition.

This interesting question is from Iterative Methods of Multiple Sequence Alignment topic in section Multiple Sequence Alignment of Bioinformatics

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Right choice is (a) True

Best explanation: The 100 initial MSAs are scored by the sum of pairs method, except that both natural and quasi-natural gap-scoring schemes are used. Recall that the best SSP score for a MSA is the minimum one and the one that is closest to the sum of the pair-wise sequence alignment. Standard amino acid scoring matrices and gap opening and extension penalties are used.

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