Question

BLAST uses a _______ to find matching words, whereas FASTA identifies identical matching words using the _____

(a) substitution matrix, hashing procedure

(b) substitution matrix, blocks

(c) hashing procedure, substitution matrix

(d) ktups, substitution matrix

This question was addressed to me in a national level competition.

The query is from Comparison of FASTA and BLAST in section Database Similarity Searching of Bioinformatics

Answer 1

The correct choice is (a) substitution matrix, hashing procedure

Easy explanation: BLAST and FASTA have been shown to perform almost equally well in regular database searching; However, there are some notable differences between the two approaches. The major difference is in the seeding step– BLAST uses a substitution matrix to find matching words, whereas FASTA identifies identical matching words using the hashing procedure.