sequence-file-inventory-enumeration
License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution.
Summary
Systematically enumerate and cross-reference sequence files in a local repository (MIBiG's genbanks directory) against NCBI GenBank/RefSeq to identify sequences that are unavailable in public databases. This skill is essential for curating and documenting unique or restricted sequence assets.
When to use
When you maintain a repository with local sequence files and need to determine which sequences are not publicly available in NCBI GenBank/RefSeq databases—for example, to distinguish proprietary or supplementary sequence data from publicly registered entries, or to create an inventory manifest for data governance.
When NOT to use
- Input directory contains only already-validated NCBI accessions with no local sequences—use a simple accession lookup instead.
- Sequences are known to be private or restricted by license and you do not need public availability confirmation—enumeration is unnecessary overhead.
Inputs
- Local sequence file directory (e.g., genbanks directory in MIBiG repository)
- Sequence file metadata (filename, entry identifier, optional NCBI accession)
- NCBI GenBank/RefSeq database (via E-utilities or BLAST index)
Outputs
- Structured inventory manifest (CSV or JSON format)
- Manifest columns: file path, sequence identifier, GenBank accession, availability status (local-only or public)
How to apply
Clone or access the target repository (e.g., MIBiG's github.com/mibig-secmet/mibig-json) and list all sequence files in the designated directory (e.g., genbanks). For each file, extract its entry identifier and any embedded NCBI accession number. Use NCBI E-utilities or local BLAST to query whether that accession exists in GenBank/RefSeq; if no accession is present or the query returns no hit, flag it as local-only. Compile results into a structured manifest (CSV or JSON) with columns for file path, sequence identifier, GenBank accession (if present), and availability status (local-only or public). The rationale is to create a transparent, machine-readable record of which sequences are unique to the repository versus mirrored from public sources.
Related tools
- NCBI E-utilities (Query NCBI GenBank/RefSeq accession identifiers to determine if a sequence is publicly registered)
- BLAST (Local or remote sequence similarity search to cross-reference local sequences against GenBank/RefSeq and confirm accession status)
Evaluation signals
- Manifest file exists and contains all expected columns (file path, sequence identifier, GenBank accession, availability status).
- No sequence files from the input directory are missing from the manifest; row count equals file count.
- For each row marked 'public', the GenBank accession field is non-empty and validated; for 'local-only' rows, accession is empty or null.
- Spot-check: manually verify 3–5 flagged 'local-only' sequences by querying NCBI directly; no false negatives (sequences marked local but actually public in GenBank).
- Manifest is well-formed JSON or valid CSV with no malformed cells or unexpected null values.
Limitations
- NCBI E-utilities queries may have rate limits or temporary unavailability; plan for retry logic or fallback to manual spot-checks.
- Sequences without embedded NCBI accessions cannot be definitively cross-referenced unless you perform full BLAST alignment, which is slower and may not always yield a clear match.
- The MIBiG repository maintains only 'a handful' of local sequences, so the inventory may be small and may not justify high automation investment.
- Accession identifiers may be outdated or withdrawn from NCBI; the manifest reflects status at query time only.
Evidence
- [readme] The
genbanks directory contains a handful of sequence files that are not available from NCBI's GenBank/RefSeq databases: "The genbanks directory contains a handful of sequence files that are not available from NCBI's GenBank/RefSeq databases."
- [other] Scan the genbanks directory, cross-reference against NCBI accession identifiers, and compile results into a structured manifest: "Scan the
genbanks directory to list all sequence files and their metadata. 3. Cross-reference each file against NCBI GenBank/RefSeq accession identifiers (using NCBI E-utilities or local BLAST) to"
- [other] Output should be CSV or JSON with columns for file path, sequence identifier, GenBank accession, and availability: "Output the manifest as a CSV or JSON file with columns for file path, sequence identifier, GenBank accession, and availability (local-only or public)."
- [other] Tools to use for cross-referencing and validation: "tools: NCBI E-utilities, BLAST"
1---2name: sequence-file-inventory-enumeration3description: Use when when you maintain a repository with local sequence files and need to determine which sequences are not publicly available in NCBI GenBank/RefSeq databases—for example, to distinguish proprietary or supplementary sequence data from publicly registered entries, or to create an inventory.4license: CC-BY-4.05---67# sequence-file-inventory-enumeration89> **License: restricted** — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. <!-- asb-license-banner -->10## Summary1112Systematically enumerate and cross-reference sequence files in a local repository (MIBiG's genbanks directory) against NCBI GenBank/RefSeq to identify sequences that are unavailable in public databases. This skill is essential for curating and documenting unique or restricted sequence assets.1314## When to use1516When you maintain a repository with local sequence files and need to determine which sequences are not publicly available in NCBI GenBank/RefSeq databases—for example, to distinguish proprietary or supplementary sequence data from publicly registered entries, or to create an inventory manifest for data governance.1718## When NOT to use1920- Input directory contains only already-validated NCBI accessions with no local sequences—use a simple accession lookup instead.21- Sequences are known to be private or restricted by license and you do not need public availability confirmation—enumeration is unnecessary overhead.2223## Inputs2425- Local sequence file directory (e.g., genbanks directory in MIBiG repository)26- Sequence file metadata (filename, entry identifier, optional NCBI accession)27- NCBI GenBank/RefSeq database (via E-utilities or BLAST index)2829## Outputs3031- Structured inventory manifest (CSV or JSON format)32- Manifest columns: file path, sequence identifier, GenBank accession, availability status (local-only or public)3334## How to apply3536Clone or access the target repository (e.g., MIBiG's github.com/mibig-secmet/mibig-json) and list all sequence files in the designated directory (e.g., `genbanks`). For each file, extract its entry identifier and any embedded NCBI accession number. Use NCBI E-utilities or local BLAST to query whether that accession exists in GenBank/RefSeq; if no accession is present or the query returns no hit, flag it as local-only. Compile results into a structured manifest (CSV or JSON) with columns for file path, sequence identifier, GenBank accession (if present), and availability status (local-only or public). The rationale is to create a transparent, machine-readable record of which sequences are unique to the repository versus mirrored from public sources.3738## Related tools3940- **NCBI E-utilities** (Query NCBI GenBank/RefSeq accession identifiers to determine if a sequence is publicly registered)41- **BLAST** (Local or remote sequence similarity search to cross-reference local sequences against GenBank/RefSeq and confirm accession status)4243## Evaluation signals4445- Manifest file exists and contains all expected columns (file path, sequence identifier, GenBank accession, availability status).46- No sequence files from the input directory are missing from the manifest; row count equals file count.47- For each row marked 'public', the GenBank accession field is non-empty and validated; for 'local-only' rows, accession is empty or null.48- Spot-check: manually verify 3–5 flagged 'local-only' sequences by querying NCBI directly; no false negatives (sequences marked local but actually public in GenBank).49- Manifest is well-formed JSON or valid CSV with no malformed cells or unexpected null values.5051## Limitations5253- NCBI E-utilities queries may have rate limits or temporary unavailability; plan for retry logic or fallback to manual spot-checks.54- Sequences without embedded NCBI accessions cannot be definitively cross-referenced unless you perform full BLAST alignment, which is slower and may not always yield a clear match.55- The MIBiG repository maintains only 'a handful' of local sequences, so the inventory may be small and may not justify high automation investment.56- Accession identifiers may be outdated or withdrawn from NCBI; the manifest reflects status at query time only.5758## Evidence5960- [readme] The `genbanks` directory contains a handful of sequence files that are not available from NCBI's GenBank/RefSeq databases: "The `genbanks` directory contains a handful of sequence files that are not available from NCBI's GenBank/RefSeq databases."61- [other] Scan the genbanks directory, cross-reference against NCBI accession identifiers, and compile results into a structured manifest: "Scan the `genbanks` directory to list all sequence files and their metadata. 3. Cross-reference each file against NCBI GenBank/RefSeq accession identifiers (using NCBI E-utilities or local BLAST) to"62- [other] Output should be CSV or JSON with columns for file path, sequence identifier, GenBank accession, and availability: "Output the manifest as a CSV or JSON file with columns for file path, sequence identifier, GenBank accession, and availability (local-only or public)."63- [other] Tools to use for cross-referencing and validation: "tools: NCBI E-utilities, BLAST"
HolobiomicsLab