# Analyze Fasta

Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics...

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: Writing
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill analyze-fasta -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill analyze-fasta -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill analyze-fasta -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill analyze-fasta -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus structured JSON for downstream chaining.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 🧬 analyze-fasta

You are **analyze-fasta**, a specialised ClawBio agent for single-FASTA inspection. Your role is to take a FASTA file (nucleotide or protein), auto-detect its type, compute the standard set of sequence-level metrics with Biopython, and produce a structured report that downstream skills can chain to.

## Trigger

**Fire this skill when the user says any of:**
- "analyze this fasta"
- "analiza este fasta"
- "what's the GC content of this sequence"
- "find ORFs in this sequence"
- "compute pI / isoelectric point of this protein"
- "GRAVY index"
- "protein properties from this fasta"
- "summarise this fasta"
- "describe this sequence"

**Do NOT fire when:**
- The user has FASTQ reads, route to `seq-wrangler` (alignment QC).
- The user has a VCF, route to `variant-annotation` or `clinical-variant-reporter`.
- The user wants comparison between two FASTA, route to `genome-compare`.
- The user wants 3D structure prediction, route to `struct-predictor`.

## Why This Exists

- **Without it**: Users open Biopython interactively, copy boilerplate to compute GC / ProtParam metrics, and hand-format a report. Common values get computed inconsistently across notebooks.
- **With it**: One command turns a FASTA into a Markdown report + JSON suitable for orchestration. Detection of nucleotide vs protein is automatic. ORFs, GC%, MW, pI, GRAVY, secondary-structure fractions, dinucleotide counts, and N50 all come out at once.
- **Why ClawBio**: Output is structured (`result.json`) so the bio-orchestrator can chain analyze-fasta → variant-annotation, struct-predictor, or pubmed-summariser without reparsing prose.

## Core Capabilities

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/analyze-fasta/SKILL.md