TBLASTX

TBLASTX is a nucleotide-to-protein translation search tool in the BLAST family used to detect distant relationships between nucleotide sequences. It compares six-frame translations of a nucleotide query sequence against six-frame translations of a nucleotide database, effectively performing a protein–level comparison rather than a direct nucleotide alignment.

How it works: For both the query and the database, all six possible reading frames are translated into amino acid sequences. The resulting protein sequences are then compared using a protein scoring matrix and a heuristic search to identify high-scoring segment pairs, which are extended to local alignments. The results report statistics such as bit score and E-value, along with details about the corresponding nucleotide coordinates and reading frames.

Limitations and considerations: TBLASTX is computationally intensive because it evaluates translations in six frames for both query and database, making it slower and more resource-demanding than nucleotide-nucleotide or protein-protein BLAST searches. It can be influenced by low-complexity regions, and its effectiveness depends on the evolutionary distance and the quality of the translated alignments. The method emphasizes amino acid similarity, which helps reveal distant homology but may overlook short or highly divergent regions.

Applications: It is commonly used to detect homologous genes in genomic and metagenomic data, annotate novel genomes, and identify conserved protein-coding regions across divergent taxa where direct nucleotide similarity is weak. TBLASTX is available as part of the NCBI BLAST toolkit and can be accessed via web interfaces or programmatic APIs.