GATE 2023 BT, question 26: Bioinformatics — solution and answer

Official key: C · Official answer key, GATE 2023 BT (IIT Kanpur)

1. BLASTN aligns a nucleotide query against a nucleotide database; it does not address protein homology at all, so it is not the tool sought here.

2. BLASTX translates a nucleotide query (all six reading frames) and searches it against a protein database in a single-pass alignment — useful for identifying a likely protein match but not specialized for remote/distant homology detection.

3. TBLASTX translates both the nucleotide query and a nucleotide database (six frames on each side) and compares the translated sequences — again a single, direct alignment pass; computationally heavy but not iterative, so it offers no special sensitivity boost for remote homologs.

4. PSI-BLAST (Position-Specific Iterated BLAST) runs an initial BLAST search, then builds a position-specific scoring matrix (profile) from the statistically significant hits, and repeats the profile search over multiple iterations.

5. This iterative, profile-based refinement is precisely what amplifies weak or distant sequence similarity signals that a single-pass alignment (as in A, B, D) would miss, making PSI-BLAST the standard choice for detecting distantly related (remote) protein homologs.

6. Therefore option (C) PSI-BLAST is correct; options (A) BLASTN, (B) BLASTX, and (D) TBLASTX are each single-pass tools not designed for remote homology detection.