Hmmbuild

hmmbuild

Quick Start

• Command: hmmbuild [options] <hmm_out> <msa_file>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hmmbuild
• Package: HMMER 3.4
• Reference: See references/help.md for the current startup failure; option details below are grounded in the local man page

When To Use This Tool

• Build a profile HMM from a curated multiple-sequence alignment.
• Create the model that will later be searched with hmmsearch.
• Turn seed alignments into reusable family or domain detectors.
• Use only when the alignment quality is good enough to justify a model.

Common Patterns

# Build a profile HMM from one curated alignment
hmmbuild kinase.hmm kinase_alignment.sto

# Force nucleotide alphabet when autodetection would be ambiguous
hmmbuild --dna dna_family.hmm dna_alignment.sto

# Save the annotated Stockholm alignment that hmmbuild actually used
hmmbuild -O annotated.sto family.hmm seed_alignment.sto

# Name a single model explicitly
hmmbuild -n KinaseDomain kinase.hmm kinase_alignment.sto

Recommended Workflow

1. Start from a real multiple-sequence alignment, not raw unaligned FASTA.
2. Inspect the alignment for bad fragments, frameshifts, or unrelated sequences before model building.
3. Decide whether consensus columns should be inferred automatically (--fast, default) or taken from reference annotation (--hand).
4. Build the HMM, and optionally capture the annotated Stockholm alignment with -O so you can review weights and chosen consensus columns.
5. Test the resulting model with hmmsearch or hmmstat, then run hmmpress if the model will become part of a scan database.

Guardrails

• The input must be an alignment, not a bag of unaligned sequences.
• Garbage in, garbage out: poor alignment quality produces misleading models.
• On this workstation, the current local binary is presently failing with a missing libopenblas.so.0; use the local man page conservatively until that library issue is fixed.
• msa_file may be - to read from stdin, but hmm_out cannot be - because stdout is used for other textual output.
• -n only applies when building a single alignment; with multi-alignment input, each alignment needs its own annotated name.
• --hand relies on reference annotation already present in the alignment.
• Keep model validation separate from model construction so thresholds can be tuned honestly.