Question

In sequence alignment by BLAST, each word from query sequence is typically _______ residues for protein sequences and _______ residues for DNA sequences.

(a) ten, eleven

(b) three, three

(c) three, eleven

(d) three, ten

I got this question in final exam.

My question is taken from Basic Local Alignment Search Tool (BLAST) topic in division Database Similarity Searching of Bioinformatics

Answer 1

The correct option is (c) three, eleven

For explanation: The first step is to create a list of words from the query sequence. Each word is typically three residues for protein sequences and eleven residues for DNA sequences. The list includes every possible word extracted from the query sequence. This step is also called seeding.