Question

Gaps are added to the alignment because it ______

(a) increases the matching of identical amino acids at subsequent portions in the alignment

(b) increases the matching of or dissimilar amino acids at subsequent portions in the alignment

(c) reduces the overall score

(d) enhances the area of the sequences

The question was asked in exam.

I would like to ask this question from Dynamic Programming Algorithm for Sequence Alignment topic in division Sequence Alignment of Bioinformatics

Answer 1

The correct choice is (a) increases the matching of identical amino acids at subsequent portions in the alignment

Explanation: In the alignment process, gaps are added to the alignment in a manner that increases the matching of identical or similar amino acids at subsequent portions in the alignment. Ideally, when two similar protein sequences are aligned, the alignment should have long regions of identical or related amino acid pairs and very few gaps. As the sequences become more distant, more mismatched amino acid pairs and gaps should appear.