Use when searching protein queries against translated SRA or WGS-backed VDB databases with BLAST.
tblastn_vdb -query proteins.fa -db <SRA_or_WGS_name> [options]/home/vimalinx/miniforge3/envs/bio/bin/tblastn_vdbtblastn-style searches without first building a local translated BLAST database.-sra_mode.-matrix, -evalue, -comp_based_stats, or -in_pssm.# 1) Search unaligned reads only with tabular output
tblastn_vdb \
-query proteins.fa \
-db SRR123456 \
-sra_mode 0 \
-outfmt 6 \
-evalue 1e-6 \
-num_threads 8
# 2) Search aligned reference sequences only
tblastn_vdb \
-query proteins.fa \
-db SRR123456 \
-sra_mode 1 \
-out aligned_refs.txt
# 3) Include filtered reads and search from a PSI-BLAST checkpoint
tblastn_vdb \
-in_pssm profile.chk \
-db SRR123456 \
-sra_mode 2 \
-include_filtered_reads \
-outfmt "6 qaccver saccver pident length evalue bitscore"
-sra_mode explicitly.-outfmt, -evalue, -matrix, -comp_based_stats, and -num_threads.-db here means an SRA or WGS database name; it is not a standard local BLAST DB path.-help and -version; autogenerated --help or --version captures are wrong for the live binary.Must specify at least one SRA/WGS database, so missing -db is the first thing to check.-sra_mode 0 searches unaligned reads only, 1 searches aligned reference sequences only, and 2 searches both; record that choice in reproducible workflows.-query and -in_pssm are mutually exclusive, and -db_gencode matters if the subject database needs a non-standard translation table.