Blastdbcmd

blastdbcmd

Quick Start

• Command: blastdbcmd
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blastdbcmd
• Version: 2.17.0+
• Full reference: See references/help.md for complete options

When To Use This Tool

• Inspect a BLAST database after building it.
• Retrieve one or many sequences by identifier from a local BLAST DB.
• Export taxonomy summaries or database metadata.
• Sanity-check that makeblastdb produced what your pipeline expects.

Common Patterns

# 1) Inspect database metadata
blastdbcmd -db proteins_db -info

# 2) Retrieve one entry in FASTA format
blastdbcmd \
  -db proteins_db \
  -entry XP_123456.1 \
  -outfmt "%f"

# 3) Retrieve many entries from a batch file
blastdbcmd \
  -db proteins_db \
  -entry_batch ids.txt \
  -outfmt "%f" \
  -out hits.fa

# 4) Export taxonomy summary
blastdbcmd -db proteins_db -tax_info

Recommended Workflow

1. Use -info first to confirm the database type and metadata.
2. Retrieve by -entry or -entry_batch only if the DB was built with usable sequence IDs.
3. Use -outfmt deliberately; %f is the common FASTA choice for sequence export.
4. For taxonomic inspection, use -tax_info rather than trying to parse raw metadata blobs.

Guardrails

• -entry, -entry_batch, -info, -metadata, and -tax_info are mutually exclusive modes.
• Range and strand selection only make sense for nucleotide sequence retrieval.
• -entry all can dump an entire database, which is often much larger than expected.
• If retrieval by accession fails, the underlying DB may have been built without -parse_seqids.