blastx

Translated nucleotide-to-protein sequence search

TLDR

Search translated nucleotide against protein database

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

Output in tabular format

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

Output in XML format

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

Set E-value threshold

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

Limit number of alignments

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

Use multiple threads

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

Show help

$ blastx -help

SYNOPSIS

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.

PARAMETERS

-query file

Input nucleotide sequence file (FASTA format)

-db name

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

-out file

Output file for results

-outfmt format

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

-evalue value

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

-max_target_seqs n

Maximum number of aligned sequences to keep

-num_threads n

Number of threads/CPUs to use

-word_size n

Word size for initial match

-matrix name

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

-query_gencode n

Genetic code for query translation (default: 1).

-seg method

Filter query sequence for low-complexity regions (default: 12 2.2 2.5).

-task name

Task to execute: blastx (default) or blastx-fast.

-remote

Execute search remotely on NCBI servers.

INSTALL

sudo apt install ncbi-blast+

CAVEATS

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.

HISTORY

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.