Question

Which of the following is untrue regarding the gap penalty used in dynamic programming?

(a) Gap penalty is subtracted for each gap that has been introduced

(b) Gap penalty is added for each gap that has been introduced

(c) The gap score defines a penalty given to alignment when we have insertion or deletion

(d) Gap open and gap extension has been introduced when there are continuous gaps (five or more)

I had been asked this question during an interview for a job.

My question comes from Local Sequence Alignment topic in chapter Sequence Alignment of Bioinformatics

Answer 1

The correct option is (b) Gap penalty is added for each gap that has been introduced

Best explanation: Dynamic programming algorithms use gap penalties to maximize the biological meaning. The open penalty is always applied at the start of the gap, and then the other gaps following it is given with a gap extension penalty which will be less compared to the open penalty. Typical values are –12 for gap opening, and –4 for gap extension.