hmmsearch

name	hmmsearch
description	Use when searching profile hidden Markov models against sequence databases to identify homologous sequences or protein family members
disable-model-invocation	true
user-invocable	true

hmmsearch

Quick Start

• Command: hmmsearch [options] <hmmfile> <seqdb>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hmmsearch
• Version: HMMER 3.4
• Full reference: See references/help.md for detailed options and usage

When To Use This Tool

• Search one or more profile HMMs against a sequence database.
• Identify homologous proteins from a family or domain model.
• Prefer hmmsearch when the query is the model and the target is a sequence set.
• Prefer hmmscan when the query is the sequence set and the target is the HMM database.

Common Patterns

# 1) Search one HMM against a protein FASTA database
hmmsearch \
  --tblout hits.tbl \
  --domtblout domains.tbl \
  --cpu 8 \
  kinase.hmm \
  proteome.fa

# 2) Use curated Pfam-style thresholds when the HMM provides them
hmmsearch \
  --cut_ga \
  --tblout hits.tbl \
  profile.hmm \
  targets.fa

# 3) Increase sensitivity by disabling heuristics
hmmsearch \
  --max \
  --domtblout domains.tbl \
  profile.hmm \
  targets.fa

Recommended Workflow

1. Start from a trusted HMM built from a good alignment or downloaded from a curated source.
2. Save parseable output with --tblout and --domtblout; do not rely on plain-text reports alone.
3. Choose thresholding deliberately: generic E-values or curated --cut_ga, --cut_tc, or --cut_nc.
4. Review both per-sequence and per-domain significance before claiming family membership.

Guardrails

• Positional argument order matters: <hmmfile> first, then <seqdb>.
• Use -h for help; --help and --version are not valid here.
• --max improves sensitivity but can slow searches down substantially.
• Save table outputs whenever results will be parsed or compared across runs.