Question

In the GCG and FASTA program suites, the scoring matrix itself is formatted in a way that includes default ______

(a) gap additions

(b) alignment scores

(c) score penalties

(d) gap penalties

This question was posed to me during an online exam.

My doubt stems from Use of Scoring Matrices and Gap Penalties in Sequence Alignments in chapter Sequence Alignment of Bioinformatics

Answer 1

Correct answer is (d) gap penalties

Best explanation: These program suites include default gap penalties. When deciding gap penalties for local alignment programs, a consideration is that the penalties should be large enough to provide a local alignment of the sequences.