What is bio-remote-homology?

A guide to finding distant homologs—proteins or genes related by evolution—when ordinary BLAST searches miss them. It covers profile-based and structure-based searches, including HMMER, MMseqs2, DIAMOND, and Foldseek.

Use it to search protein or gene sequences, compare metagenomic data, build homology searches, and find related structures.

It helps recover relationships hidden by low sequence similarity and choose a suitable search method and database for large or difficult comparisons.

bio-remote-homology — Skill for Claude Code and Codex by GPTomics

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add GPTomics/bioSkills --skill remote-homology

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/remote-homology/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/remote-homology)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/remote-homology"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/remote-homology/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/remote-homology"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/remote-homology.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 132 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 5,194 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00132	$0.05194
Opus 5	$0.00066	$0.02597
Sonnet 5	$0.00026	$0.01039
Haiku 4.5	$0.00013	$0.00519

Measured 8d ago against content hash b75e3c1cc62a, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-11, from the pricing page.

Security

Grade A, and why

bio-remote-homology scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.

The scan reads SKILL.md. This mod also ships 3 executable files (examples/foldseek_search.sh, examples/iterative_profile.sh, examples/pfam_annotation.sh), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-remote-homology — 95% identical, 12 lines differ

database-access/remote-homology/SKILL.md · 360 lines

How it starts

The opening of the file, as written. The whole thing — 360 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: NCBI BLAST+ 2.15+, HMMER 3.4+, MMseqs2 15+, DIAMOND 2.1+, HH-suite3 3.3+, Foldseek 9+

Before using code patterns, verify installed versions match. If versions differ:

CLI: <tool> --version then <tool> --help to confirm flags
Python: pip show <package> then introspect signatures

If a flag is unrecognized or behavior changes, introspect with --help and adapt the example to match the installed version rather than retrying.

Remote Homology

"Find homologs my BLAST missed" -> Standard BLAST detects similarity reliably down to ~35% pairwise identity (the "twilight zone", Rost 1999 Protein Eng 12:85). Below that, profile methods (PSSMs, HMMs) and structure-aware methods (Foldseek) recover homologs that pairwise alignment misses.

This skill covers the decision: which method, when, against what database. The competition has shifted substantially since 2015: PSI-BLAST is no longer the de-facto standard; MMseqs2 and DIAMOND have replaced BLAST in most large-scale workflows; Foldseek (van Kempen et al. 2024 Nat Biotechnol 42:243) detects homologs no sequence method can reach by searching with a 3Di structural alphabet derived from AlphaFold/ESMFold predictions.

CLI: psiblast, jackhmmer, hmmsearch, hhblits, mmseqs, diamond, foldseek
Python: Bio.SearchIO for output parsing; tool-specific clients exist but subprocess is preferred
Web: HHpred (HHblits webserver), Foldseek webserver, ColabFold for paired structure search

Required Setup

# Install via conda
conda install -c bioconda hmmer mmseqs2 diamond hhsuite foldseek
# BLAST+ (separate)
conda install -c bioconda blast

# Verify
hmmsearch -h | head -3       # HMMER 3.4+
mmseqs version               # MMseqs2 15+
diamond --version            # DIAMOND 2.1+
hhblits -h | head -3         # HH-suite3 3.3+
foldseek --version           # Foldseek 9+

Decision matrix: which method when

Question	Best tool	Why	Sensitivity / Speed
Quick all-vs-all proteome	MMseqs2 or DIAMOND	100-10,000x faster than BLAST at comparable sensitivity	Highest throughput, near-BLAST sensitivity
Identify distant protein homolog (single query)	jackhmmer	Iterative HMM; usually beats PSI-BLAST	Higher sensitivity than PSI-BLAST
Distant homology where structure available	Foldseek	3Di alphabet finds homologs sequence misses	Finds hits PSI-BLAST/HMMER cannot
Profile-profile comparison (PDB70 / Pfam)	HHblits + HHsearch	Profile vs profile is most sensitive when target also has profile	Best sensitivity for very-deep homology
Domain assignment	hmmscan against Pfam-A	Curated, calibrated thresholds	Standard practice
Metagenomic protein clustering	MMseqs2 `easy-cluster`	Scales to >1B sequences	Production-grade
ORF search vs metagenome	DIAMOND `blastx --frameshift`	Frameshift-aware; long reads	Best for noisy long reads
Structure-aware homology (no AF2 prediction available)	Foldseek + ProstT5	Predicts 3Di alphabet from sequence via PLM	Skip the AF2 step

Read the full file on GitHub · 360 lines

Files

What ships with it

4 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

8d ago First seen · 360 lines · 132 tokens per session scan A b75e3c1cc62a

Subscribe to this mod's changes

bio-remote-homology is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 132 tokens to every session and 5,194 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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bio-remote-homology