Question

Which of the following is incorrect the ‘word’ method?

(a) Both BLAST and FASTA use a heuristic word method

(b) Word method is used for fast pairwise sequence alignment in BLAST and FASTA

(c) The basic assumption is that two related sequences must have at least one word in common

(d) Two related sequences must have at zero word in common while assuming

The question was asked during an interview.

The question is from Heuristic Database Searching topic in division Database Similarity Searching of Bioinformatics

Answer 1

Right option is (d) Two related sequences must have at zero word in common while assuming

Explanation: This is the third method of pairwise sequence alignment. It works by finding short stretches of identical or nearly identical letters in two sequences. These short strings of characters are called words, which are similar to the windows used in the dot matrix method. The basic assumption is that two related sequences must have at least one word in common. By first identifying word matches, a longer alignment can be obtained by extending similarity regions from the words. Once regions of high sequence similarity are found, adjacent high-scoring regions can be joined into full alignment.