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

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.