Question

Like other alignment programs, CLUSTAL uses a null score for opening a gap in a sequence alignment and a penalty for extending the gap by one residue.

(a) True

(b) False

The question was posed to me during an interview.

The query is from Progressive Methods of Multiple Sequence Alignment topic in chapter Multiple Sequence Alignment of Bioinformatics

Answer 1

Correct answer is (b) False

For explanation: CLUSTAL uses a penalty for opening a gap in a sequence alignment and an additional penalty for extending the gap by one residue. These penalties are user-defined. Gaps found in the initial alignments remain fixed. New gaps introduced as more sequences are added also receive this same gap penalty, even when they occur within an existing gap, but the gap penalties for alignment are then modified according to the average match value in the substitution matrix, the percent identity between the sequences, and the sequence lengths.