hmmer-profile-search
Validate and run bounded local HMMER3 profile-to-protein searches with domain coordinates, explicit thresholds, researcher approval and auditable outputs.
Skill by phenixace
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Install
Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.
npx agentmarket install skill/phenixace-hmmer-profile-search
Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.
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About
Use cases: backend
Reviews
Write a reviewNo reviews yet. Installed it? Reviews come from verified installers only. How reviews work
Permissions
What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.
- Tools
- No tools found
- Secrets
- None asked for
- Install scripts
- None found
- Runs as
- Python package
Network hosts it talks to 1
codeload.github.com· found in install command
Files it touches
~/.claude/skills/hmmer-profile-search
What's inside
- Skill name
hmmer-profile-search- Description
- Validate and run bounded local HMMER3 profile-to-protein searches with domain coordinates, explicit thresholds, researcher approval and auditable outputs. Use when the user supplies an amino-acid profile HMM and a workspace protein FASTA database; not for downloading Pfam, asserting function from a match, or unbounded remote searches.
- License
- MIT
- Instructions
- 11 lines in SKILL.md · view on GitHub
Before installing
- Ships executable scripts
Files (4)
- SKILL.md
- openai.yaml · agents/
- handler.py · scripts/
- skill.json
SKILL.md (first lines)
# HMMER Profile Search Use `hmmer_profile_preflight` before proposing execution. Confirm the exact HMM and protein FASTA paths, model identities, model and database sizes, sequence and domain E-value reporting thresholds, hit limit, HMMER version and runtime availability. Use `hmmer_profile_search` only through a researcher-approved workflow. Preserve profile and target names, full-sequence E-value and score, domain conditional and independent E-values, HMM coordinates, target alignment and envelope coordinates, accuracy, bias, input hashes and output paths. `--domE` is a conditional E-value reporting threshold; never label it as the independent E-value threshold. HMMER E-values depend on the search space and profile. A profile match supports sequence-family or domain relatedness; it does not by itself prove molecular function, mechanism, activity, localization or phenotype. Review domain coverage, repeat architecture, composition bias, profile construction and independent evidence. The workflow accepts bounded local HMMER3 amino-acid profiles and protein FASTA files. It does not download or version Pfam, execute arbitrary commands, search remote databases, build profiles from alignments, or convert hits into functional annotations.
From phenixace/Molemo_WorkBench, MIT.
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- 0.557score
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Turn molecular and protein analysis results into declarative property charts and residue-level sequence tracks.
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protein-structure
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Retrieve experimental structures from RCSB PDB, predicted structures from AlphaFold DB, or parse PDB/mmCIF files in the local workspace.
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guided-workflows
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Create reviewable, researcher-approved plans from Molemo scientific tools.
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Route broad life-science research questions to the smallest useful set of Molemo skills.
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chembl-bioactivity
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sequence-search
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Search one concrete protein or nucleotide sequence against a FASTA database inside the local Molemo workspace with NCBI BLAST+.
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single-cell-analysis
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clinical-trial-landscape
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Search ClinicalTrials.gov for a bounded trial landscape or review the posted tabular results of one exact NCT record.
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dna-variant-calling
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Preflight and run a bounded, researcher-approved paired-end short-read DNA alignment and candidate variant-calling workflow with local BWA, samtools, and…
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functional-analysis
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Review a bounded human gene set with Reactome pathway overrepresentation and STRING identifier mapping, enrichment, functional association networks, and PPI…
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Signals
- Stars
- 2
- Forks
- 0
- Open issues
- 0
- Last commit (this folder)
- Aug 29, 2026 (2 months ago)
From GitHub (fetched Oct 24, 2026).
Details
- License
- MIT
- Repository
- github.com/phenixace/Molemo_WorkBench
- First seen
- Oct 24, 2026
- Last checked
- Oct 24, 2026
- Source
- GitHubgithub-graphql
More from phenixace
- 0.557score
research-router
phenixace
Route broad life-science research questions to the smallest useful set of Molemo skills.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
guided-workflows
phenixace
Create reviewable, researcher-approved plans from Molemo scientific tools.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
chembl-bioactivity
phenixace
Review source-linked ChEMBL small-molecule activity evidence for an exact UniProt single-protein target.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
protein-structure
phenixace
Retrieve experimental structures from RCSB PDB, predicted structures from AlphaFold DB, or parse PDB/mmCIF files in the local workspace.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
scientific-visualization
phenixace
Turn molecular and protein analysis results into declarative property charts and residue-level sequence tracks.
SkillBFreshness: B★ 2Claude Code +9 - 0.554score
public-databases
phenixace
Retrieve named compounds from PubChem and protein records from UniProt using fixed official API hosts.
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Cite this page
hmmer-profile-search skill. Agent Mart. https://agentmart.dev/skills/phenixace-hmmer-profile-search (last updated 2026-10-24)