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bio-annotation

Annotate protein functions and taxonomy from sequence homology using InterProScan, eggNOG-mapper, DIAMOND, and TaxonKit.

7|1|Updated Feb 2, 2026
Search Tags:#taxonomy#annotation#diamond#protein-function#interproscan#eggnog-mapper#taxonkit
One-click install
npx skills add https://github.com/fmschulz/omics-skills --skill bio-annotation
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-annotation
Source: https://github.com/fmschulz/omics-skills/tree/main/skills/bio-annotation
Command: npx skills add https://github.com/fmschulz/omics-skills --skill bio-annotation

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Annotation of protein functions and taxonomy from sequence homology to accelerate omics analyses.

Core Features & Use Cases

  • InterProScan for domain/family annotation
  • eggNOG-mapper for orthology-based annotation
  • DIAMOND with TaxonKit for taxonomy inference
  • Input: proteins.faa and reference_db directories
  • Output: results/bio-annotation/ with annotation reports and taxonomy tables

Quick Start

Run the bio-annotation workflow with your proteins.faa and reference databases to generate functional annotations and taxonomy results.

Frequently Asked Questions about bio-annotation

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate protein function annotation for omics workflows?▼

You can automate protein function annotation by running sequence homology workflows that integrate InterProScan, eggNOG-mapper, and DIAMOND to generate domain, orthology, and functional reports from your input proteins.

How does sequence homology-based taxonomy inference work with DIAMOND and TaxonKit?▼

Taxonomy inference uses DIAMOND to match input protein sequences against reference databases, then applies TaxonKit to resolve and map the resulting hits into structured taxonomic lineages and tables.

What input format is needed to run InterProScan and eggNOG-mapper for protein annotation?▼

You need a FASTA amino acid file, typically named proteins.faa, and appropriately configured reference database directories to execute the InterProScan and eggNOG-mapper annotation pipeline.

Can I use eggNOG-mapper and InterProScan together in a single protein annotation pipeline?▼

Yes, this pipeline integrates both tools to provide comprehensive protein annotation, combining eggNOG-mapper for orthology-based functional inferences and InterProScan for domain and family annotation in one workflow.

What is the best way to generate taxonomy tables from protein sequences?▼

The best way to generate taxonomy tables is using a combined DIAMOND and TaxonKit workflow that processes your protein sequences against reference databases and outputs structured taxonomy resolution files.

What outputs should I expect from an automated protein function and taxonomy annotation workflow?▼

Automated protein annotation workflows output detailed functional annotation reports from InterProScan and eggNOG-mapper, alongside resolved taxonomy tables generated by DIAMOND and TaxonKit, stored in a dedicated results directory.

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