Q.42 Which one of the following tools is used to compare all the possible six-open
reading frames of a given nucleotide query sequence with all the available
six-open reading frames of the nucleotide sequence database?
(A) BLASTN
(B) BLASTX
(C) TBLASTN
(D) TBLASTX
Which Tool Compares Six Reading Frames of Nucleotide Query to Database?
TBLASTX is the tool that compares all possible six open reading frames of a nucleotide query sequence with all available six open reading frames from a nucleotide sequence database. This makes it ideal for detecting distant homologies in unannotated genomic or EST data. The correct answer to the query is (D) TBLASTX.
Correct Answer
TBLASTX translates both the nucleotide query and nucleotide database sequences into all six reading frames (three forward and three reverse) before performing protein-level alignments. This exhaustive 6×6 (36 total) comparison detects evolutionary relationships obscured at the DNA level due to codon degeneracy. It is computationally intensive but highly sensitive for divergent sequences.
BLASTN Overview
BLASTN directly aligns a nucleotide query sequence against a nucleotide database without translation. It uses forward and reverse-complement strands but ignores reading frames, making it fast for highly similar DNA matches like PCR primers or genomic regions. This tool suits queries needing nucleotide-level precision, not protein predictions.
BLASTX Details
BLASTX translates the nucleotide query into six reading frames and compares these to a protein database. It helps predict gene function from raw DNA/EST by finding matching proteins but does not translate the database. Use BLASTX for a nucleotide query against known proteins, not nucleotide-vs-nucleotide frame searches.
TBLASTN Function
TBLASTN takes a protein query and translates the nucleotide database into all six reading frames for alignment. This identifies genomic regions encoding similar proteins, useful for finding genes in unannotated DNA. Unlike the query, it does not involve translating both sequences’ frames.
When to Use Each Tool
| Tool | Query Type | Database Type | Translates Query? | Translates DB? | Best For |
|---|---|---|---|---|---|
| BLASTN | Nucleotide | Nucleotide | No | No | Identical DNA sequences |
| BLASTX | Nucleotide | Protein | Yes (6 frames) | No | Gene prediction from DNA |
| TBLASTN | Protein | Nucleotide | No | Yes (6 frames) | Protein in genomic DNA |
| TBLASTX | Nucleotide | Nucleotide | Yes (6 frames) | Yes (6 frames) | Distant homologs |
