Makeblastdb

makeblastdb

Quick Start

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

When To Use This Tool

• Build local BLAST databases from FASTA before blastn, blastp, or tblastn.
• Create nucleotide (nucl) or protein (prot) databases with stable names.
• Enable identifier-aware retrieval with -parse_seqids.
• Attach taxonomy with -taxid or -taxid_map when downstream filtering requires it.

Common Patterns

# 1) Build a nucleotide database
makeblastdb \
  -in transcripts.fa \
  -dbtype nucl \
  -out transcripts_db \
  -parse_seqids

# 2) Build a protein database
makeblastdb \
  -in proteins.fa \
  -dbtype prot \
  -out proteins_db \
  -parse_seqids

# 3) Build a taxonomy-aware database
makeblastdb \
  -in proteins.fa \
  -dbtype prot \
  -out proteins_db \
  -parse_seqids \
  -taxid_map seqid_to_taxid.tsv

Recommended Workflow

1. Decide database molecule type up front: nucl or prot.
2. Use -parse_seqids if you will retrieve by accession or use taxonomy mapping later.
3. Keep the database basename stable so pipeline code does not chase renamed indexes.
4. Validate the created database immediately with a small BLAST query or blastdbcmd -info.

Guardrails

• -dbtype is required and must be exactly nucl or prot.
• -taxid_map requires -parse_seqids.
• BLAST DB version defaults to 5; keep that consistent across a workflow unless you have a compatibility reason not to.
• If you skip -parse_seqids, later blastdbcmd retrieval by sequence ID may be painful or impossible.