makeprofiledb

name	makeprofiledb
description	Use when creating PSSM databases for rpsblast, cobalt, or deltablast searches. Formats position-specific scoring matrices into BLAST-compatible profile databases.
disable-model-invocation	true
user-invocable	true

makeprofiledb

Quick Start

• Command: makeprofiledb -in <pssm_list> -out <db_name>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/makeprofiledb
• Version: 2.17.0+
• Full reference: See references/help.md

When To Use This Tool

• Build a BLAST-compatible profile database from a list of scoremat or PSSM files.
• Prepare RPS, DELTA, or COBALT profile databases for downstream searches or alignments.
• Package a custom domain collection so rpsblast or deltablast can use it locally.

Common Patterns

# 1) Build a reverse-position-specific domain database
makeprofiledb \
  -in pssm.list \
  -out custom_rps \
  -dbtype rps \
  -title "Custom RPS database"

# 2) Build a DELTA-BLAST profile database
makeprofiledb \
  -in pssm.list \
  -out custom_delta \
  -dbtype delta

# 3) Build from binary scoremats instead of text scoremats
makeprofiledb \
  -in binary_pssm.list \
  -binary \
  -out custom_rps

Recommended Workflow

1. Assemble a plain-text list file naming the PSSM/scoremat inputs.
2. Choose the correct output -dbtype for the downstream tool you intend to use.
3. Build the database and verify that the BLAST profile DB sidecar files were created.
4. Test the resulting profile DB with rpsblast or deltablast before distributing it further.

Guardrails

• -in is required and must point to a list file, not directly to a single PSSM payload.
• -dbtype defaults to rps; set it explicitly if you actually want delta or cobalt.
• In this tool, -force means use the command-line threshold; it is not an overwrite switch.
• -taxid and -taxid_map are mutually exclusive.
• Use -help rather than --help; --version also errors in this BLAST+ build.