blastx

Search translated nucleotide against protein database

$ blastx -query [sequences.fasta] -db [nr] -out [results.txt]

$ blastx -query [sequences.fasta] -db [swissprot] -outfmt 6 -out [results.tsv]

$ blastx -query [sequences.fasta] -db [nr] -outfmt 5 -out [results.xml]

$ blastx -query [sequences.fasta] -db [nr] -evalue [0.001] -out [results.txt]

$ blastx -query [sequences.fasta] -db [nr] -max_target_seqs [10] -out [results.txt]

$ blastx -query [sequences.fasta] -db [nr] -num_threads [8] -out [results.txt]

$ blastx -help

blastx [-query file] [-db database] [-out file] [options]

blastx translates a nucleotide query sequence in all six reading frames and searches it against a protein database. It is part of the NCBI BLAST+ suite for sequence similarity searching.
This tool is useful for identifying protein homologs of nucleotide sequences, annotating genes, and finding coding regions in DNA sequences.

-query file

Input nucleotide sequence file (FASTA format)

Protein database to search against (e.g., nr, swissprot)

Output file for results

Output format: 0=pairwise, 5=XML, 6=tabular, 7=tabular with comments

E-value threshold for reporting hits (default: 10)

Maximum number of aligned sequences to keep

Number of threads/CPUs to use

Word size for initial match

Scoring matrix (e.g., BLOSUM62, PAM250)

Genetic code for query translation (default: 1)

Requires pre-formatted BLAST databases; use makeblastdb to create them. Large databases like nr require significant disk space and memory. Translation in six frames increases computational time compared to blastn.

BLAST (Basic Local Alignment Search Tool) was originally developed at NCBI by Stephen Altschul and colleagues in 1990. The BLAST+ suite, including blastx, was released in 2009 with improved performance and new features.

blastn(1), blastp(1), tblastn(1), makeblastdb(1), blastdbcmd(1)