jackhmmer

name	jackhmmer
description	Use when running iterative sequence-to-sequence HMMER searches to expand a protein family from one or a few seed sequences against a sequence database.
disable-model-invocation	true
user-invocable	true

jackhmmer

Quick Start

• Command: jackhmmer
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/jackhmmer
• Version: HMMER 3.4
• Full reference: See references/help.md

When To Use This Tool

• Start from one or a few representative protein sequences and iteratively expand the hit set across a sequence database.
• Detect more remote homologs than a one-pass phmmer search can usually recover.
• Build an evolving alignment of accepted hits over multiple rounds before downstream model curation.
• Prefer hmmsearch when you already have a profile HMM, and hmmscan when the target is an HMM database.

Common Patterns

# 1) Iterative search with parseable hit tables
jackhmmer \
  --tblout hits.tbl \
  --domtblout domains.tbl \
  -N 5 \
  --cpu 8 \
  query.fa \
  targets.fa

# 2) Save the accepted-hit alignment from the search rounds
jackhmmer \
  -N 3 \
  -A accepted_hits.sto \
  query.fa \
  targets.fa

# 3) Tighten inclusion thresholds during iterative expansion
jackhmmer \
  -N 5 \
  --incE 1e-5 \
  --incdomE 1e-5 \
  query.fa \
  targets.fa

Recommended Workflow

1. Start from a representative protein FASTA query and a rewindable target sequence database in FASTA or another supported sequence format.
2. Save --tblout and --domtblout outputs on the first run so iteration effects are inspectable.
3. Cap the number of rounds with -N and set explicit inclusion thresholds if family drift would be costly.
4. Review accepted hits and saved alignments before promoting the result into hmmbuild or downstream annotation.

Guardrails

• In this workspace the binary currently fails to start because libopenblas.so.0 is missing, so fix the runtime environment before expecting live execution.
• jackhmmer takes positional arguments in query-then-database order; the target <seqdb> cannot be a non-rewindable stdin stream.
• This is a sequence-vs-sequence iterative searcher, not a profile-vs-sequence tool.
• jackhmmer does not accept curated --cut_ga, --cut_nc, or --cut_tc threshold modes.