Question

In case of the varying alignment, penalizing gaps heavily might occur. Then the best scoring local alignment between the sequences will be one that optimizes the score between matches and mismatches, without any gaps.

(a) True

(b) False

The question was asked during an internship interview.

My enquiry is from Use of Scoring Matrices and Gap Penalties in Sequence Alignments in division Sequence Alignment of Bioinformatics

Answer 1

Right choice is (a) True

For explanation: If both mismatches and gaps are heavily penalized, the resulting alignment will also be a local alignment that contains the longest region of exact matches. In the above two cases, the alignment score of the highest-scoring local alignment will increase as the logarithm of the length of the sequences. Under these same conditions, the score of the corresponding global alignment between the sequences will be negative.