BLASTX

BLASTX is a protein comparison tool in the BLAST family. It takes a nucleotide sequence as input, translates it in all six possible reading frames, and searches a protein sequence database for significant matches. It is commonly used when coding potential is uncertain or when only nucleotide data are available, enabling functional inference from protein homology even when no protein sequence is known.

Algorithmically, BLASTX converts the query into six translated amino acid sequences (three frames on each strand), then applies BLAST's heuristic seeding and extension to identify local alignments with protein database entries. It uses substitution matrices such as BLOSUM62 and standard gap penalties to score matches and reports statistics, including alignment score, E-value, percent identity, and the frame and positions for each hit.

Output includes a list of hits ordered by increasing E-value, with options to view alignments and download results. BLASTX is widely accessible through the NCBI BLAST web interface and the BLAST+ command-line package.

Applications include annotation of expressed sequence tags and other nucleotide sequences, gene discovery in genomes, and metagenomic studies. Related programs include BLASTP (protein against protein), BLASTN (nucleotide against nucleotide), TBLASTN (protein against six-frame translated nucleotide), and TBLASTX (six-frame translations of both query and database).