Question

The final step involves pairwise alignment by extending from the words in both directions while counting the alignment score using the same substitution matrix.

(a) True

(b) False

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

My question is based upon Basic Local Alignment Search Tool (BLAST) topic in portion Database Similarity Searching of Bioinformatics

Answer 1

Right answer is (a) True

Easy explanation: The extension continues until the score of the alignment drops below a threshold due to mismatches (the drop threshold is twenty-two for proteins and twenty for DNA). The resulting contiguous aligned segment pair without gaps is called high-scoring segment pair. In the original version of BLAST, the highest scored HSPs are presented as the final report. They are also called maximum scoring pairs.