# Genbank Accession Validation

> Use when you have a collection of sequence files (e.g., in a `genbanks` directory) and need to determine which are publicly available via NCBI and which are maintained locally only. This is critical for repositories like MIBiG that curate sequence data with mixed provenance.

- Skill: `holobiomicslab/genbank-accession-validation` (Agent Skill)
- Install (CLI): `npx skillmds@latest add holobiomicslab/genbank-accession-validation`
- Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/genbank-accession-validation/raw
- Safety review: PASS (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: CC-BY-4.0
- Author: HolobiomicsLab (https://skillmd.com/u/holobiomicslab)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/holobiomicslab/genbank-accession-validation

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# genbank-accession-validation

> **License: restricted** — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. <!-- asb-license-banner -->
## Summary

Validate whether sequence files in a local repository have corresponding entries in NCBI's GenBank/RefSeq databases by cross-referencing accession identifiers. This skill identifies sequences maintained only locally (non-NCBI) and flags their availability status for inventory tracking.

## When to use

Apply this skill when you have a collection of sequence files (e.g., in a `genbanks` directory) and need to determine which are publicly available via NCBI and which are maintained locally only. This is critical for repositories like MIBiG that curate sequence data with mixed provenance.

## When NOT to use

- The sequence files already have a pre-validated NCBI accession and you only need to retrieve metadata (use direct NCBI API fetch instead).
- You are working exclusively with sequences you know are local-only and do not need public availability confirmation.
- The input is a curated GenBank file already downloaded from NCBI (cross-validation is unnecessary).

## Inputs

- Directory path containing sequence files (e.g., `genbanks` directory)
- Sequence file metadata (filenames, embedded identifiers)
- NCBI GenBank/RefSeq accession identifiers (where present in files or metadata)

## Outputs

- Structured manifest (CSV or JSON file) with columns: file path, sequence identifier, GenBank accession, availability flag (local-only or public)
- Inventory of sequences not available from NCBI

## How to apply

First, scan the local sequence directory to extract all filenames and embedded sequence identifiers or accession numbers. For each entry, query NCBI E-utilities or perform a local BLAST search against GenBank/RefSeq to check for a match. Record the result (found in public database or local-only) in a structured manifest. The decision point is whether an NCBI accession identifier is present and resolvable; if the lookup fails or returns no hit, flag the sequence as local-only. Compile all records into a CSV or JSON manifest with columns for file path, sequence identifier, GenBank accession (if present), and availability status.

## Related tools

- **NCBI E-utilities** (Query NCBI GenBank/RefSeq databases to check accession identifier availability and retrieve record status)
- **BLAST** (Perform local sequence alignment against GenBank/RefSeq (or local mirror) to determine if a sequence exists in public databases)

## Evaluation signals

- Manifest file is generated and contains all sequence files from the input directory with no missing rows.
- Each row in the manifest has non-empty values for file path, sequence identifier, and availability flag.
- Spot-check: sequences with known NCBI accessions are marked as 'public'; sequences without accessions or failed NCBI lookups are marked as 'local-only'.
- No duplicate file paths or sequence identifiers in the manifest (uniqueness invariant).
- Cross-validation: requery a sample of 'public' accessions against NCBI E-utilities to confirm they resolve successfully.

## Limitations

- Accession identifiers may be malformed, missing, or embedded inconsistently across sequence file formats, requiring manual curation of edge cases.
- NCBI E-utilities rate limits and network delays may slow validation of large inventories; local BLAST queries require a current GenBank mirror.
- Sequences may be deposited in NCBI but not yet indexed, causing false 'local-only' classifications; periodic re-validation is recommended.
- The skill does not validate sequence content or integrity—only presence/absence in public databases.

## Evidence

- [other] Workflow step for identifying non-NCBI sequences: "The `genbanks` directory contains a handful of sequence files that are not available from NCBI's GenBank/RefSeq databases."
- [other] Research question defining the task: "Which sequence files in the `genbanks` directory are not available from NCBI's GenBank/RefSeq databases?"
- [other] Cross-referencing method: "Cross-reference each file against NCBI GenBank/RefSeq accession identifiers (using NCBI E-utilities or local BLAST) to determine availability status."
- [other] Output format specification: "Output the manifest as a CSV or JSON file with columns for file path, sequence identifier, GenBank accession, and availability (local-only or public)."