Question

What is not the query sequence in BLASTn?

• A. DNA
• B. RNA
• C. Protein
• D. tRNA

Hint:

Remember the simple rule for BLAST programs: the "n" in BLASTn stands for nucleotide.
Both the query and the database must consist of nucleotides (DNA, RNA, or tRNA).

Answer 1

The Correct Option is C

Step 1: Understanding the Concept:
The Basic Local Alignment Search Tool (BLAST) is a sequence alignment algorithm designed to compare biological query sequences against database sequences.
Different variants of BLAST are tailored to handle specific combinations of query and database types, depending on whether they consist of nucleotides or amino acids.

Step 2: Detailed Explanation:
The program BLASTn is specifically designed to perform nucleotide-versus-nucleotide searches.
In a BLASTn search, both the input query sequence and the target database must consist of nucleic acids.
DNA, RNA, and tRNA are all nucleic acid polymers composed of nucleotides, which means they can serve as valid query sequences for a BLASTn analysis.
Conversely, proteins are polypeptide chains composed of amino acids.
Because BLASTn cannot directly compare an amino acid sequence to a nucleotide database, a protein sequence cannot be used as the input query for this specific program.
To align a protein query against a nucleotide database, one must use tblastn, which translates the database sequences into amino acids in all six reading frames before performing the alignment.
Similarly, blastx is used to align a translated nucleotide query against a protein database.
Therefore, protein sequences are incompatible with the default BLASTn program.

Step 3: Final Answer:
Thus, protein is not a query sequence in BLASTn, corresponding to option (C).