Use when searching nucleotide sequences against a nucleotide database using translated protein comparison. Useful for detecting distant evolutionary relationships between nucleotide sequences.
tblastx -query <nucleotide_file> -db <nucleotide_db> -out <results>/home/vimalinx/miniforge3/envs/bio/bin/tblastxreferences/help.mdblastn is too insensitive.blastn for close nucleotide homology and blastx or tblastn when only one side should be translated.# 1) Standard translated-vs-translated search against a nucleotide BLAST database
tblastx \
-query transcripts.fa \
-db nt_db \
-outfmt "6 qaccver saccver pident length evalue bitscore qcovhsp frames" \
-evalue 1e-5 \
-max_target_seqs 20 \
-num_threads 8
# 2) One-off query-vs-subject comparison with explicit genetic codes
tblastx \
-query transcripts.fa \
-subject targets.fa \
-query_gencode 11 \
-db_gencode 11 \
-outfmt 7
# 3) Restrict query orientation when strand is known
tblastx \
-query transcripts.fa \
-db nt_db \
-strand plus \
-outfmt 6
-query_gencode and -db_gencode explicitly when organellar or nonstandard codes are plausible.-db and -subject are mutually exclusive.tblastx is computationally expensive because both sides are translated in six frames.-help rather than --help; --version also errors in this BLAST+ build.-remote is incompatible with local threading.