Question

Which of the following does not describe local alignment?

(a) A local alignment aligns a substring of the query sequence to a substring of the target sequence

(b) A local alignment is defined by maximizing the alignment score, so that deleting a column from either end would reduce the score, and adding further columns at either end would also reduce the score

(c) Local alignments have terminal gaps

(d) The substrings to be examined may be all of one or both sequences; if all of both are included then the local alignment is also global

I got this question by my school principal while I was bunking the class.

My question is taken from Local Sequence Alignment topic in chapter Sequence Alignment of Bioinformatics

Answer 1

Right choice is (c) Local alignments have terminal gaps

To explain: Local alignments never have terminal gaps, because a higher score could be obtained by deleting the gaps (which always have negative scores, i.e. penalties). In case of global alignment there are terminal gaps while analyzing.