Question

Which of the following are not related to Needleman-Wunsch alignment algorithm?

(a) Global alignment programs use this algorithm

(b) The output is a positive number

(c) Small changes in the scoring system can produce a different alignment

(d) Changes in the scoring system can produce the same alignment

This question was addressed to me in my homework.

This question is from Assessing the Significance of Sequence Alignments topic in chapter Sequence Alignment of Bioinformatics

Answer 1

Right answer is (d) Changes in the scoring system can produce the same alignment

To elaborate: In general, global alignment programs use the Needleman-Wunsch alignment algorithm and a scoring system that scores the average match of an aligned nucleotide or amino acid pair as a positive number. Hence, the score of the alignment of random or unrelated sequences grows proportionally to the length of the sequences. In addition, there are many possible different global alignments depending on the scoring system chosen, and small changes in the scoring system can produce a different alignment.