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name: database-application description: "Use Biotite database clients and external application wrappers for biological fetch/query planning, BLAST/MSA/DSSP/SRA/Vina/Tantan/ViennaRNA orchestration, and optional dependency diagnostics." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

Database and Application

Use this sub-skill when a task centers on biotite.database network services or biotite.application wrappers around web services and external command-line tools.

Route Here For

• RCSB PDB, AlphaFold DB, Entrez/NCBI, UniProt, and PubChem search/fetch planning.
• Choosing remote IDs, query objects, formats, target paths, overwrite/cache behavior, and retry/skip strategies for network work.
• BLAST web searches with BlastWebApp and NCBI request-rule expectations.
• Multiple sequence alignment wrappers for Clustal Omega, MAFFT, MUSCLE 3, and MUSCLE 5.
• DSSP secondary-structure annotation through mkdssp and the distinction from Biotite's local P-SEA-style structure helper.
• SRA reads through prefetch/fasterq-dump, repeat masking with tantan, docking with AutoDock Vina, and RNA secondary-structure tools from ViennaRNA.
• Explaining missing external binaries, wrapper lifecycle errors, timeout/cancel behavior, temporary-output contracts, and optional dependency/version differences.

Use Another Biotite Sub-skill For

• Sequence construction, symbols, annotations, local alignments, profiles, phylogeny, and analysis after remote sequence data is available: ../sequence-analysis/SKILL.md.
• In-memory AtomArray filtering, geometry, bonds, contacts, superposition, and trajectory analysis after structures are loaded: ../structure-analysis/SKILL.md.
• Parsing fetched FASTA, GenBank, PDB, PDBx/mmCIF, BinaryCIF, SDF/MOL, and trajectory files: ../file-io-formats/SKILL.md.
• PyMOL, RDKit, OpenMM, plotting, display, and visualization-oriented conversion: route to the interfaces-visualization sub-skill when available.

Start With

1. Classify the task as network database, web application, or local external executable; do not run network or external binaries unless the user/environment explicitly allows it.
2. For database work, decide the service, query/ID type, output format, target path/cache policy, and parser handoff before fetching.
3. For application wrappers, check required binaries first, construct the Biotite input objects, set all options while the app is still in CREATED state, then use start(), join(timeout=...), and result getters only after JOINED.
4. Route file parsing and downstream analysis to sibling sub-skills after the remote/application boundary is complete.
5. When dependency availability is uncertain, run the bundled no-network diagnostic instead of probing services or executing analyses.

References

• API map and ownership boundaries: references/api-reference.md.
• Database and wrapper recipes: references/workflows.md.
• Failure recovery and safe-skip guidance: references/troubleshooting.md.
• Optional dependency diagnostic: scripts/check_optional_applications.py.

Quick Dependency Check

From the Biotite skill root, run the safe diagnostic when a task depends on optional wrappers:

python sub-skills/database-application/scripts/check_optional_applications.py

The helper checks Biotite wrapper imports and executable presence/version-output probes only. It does not contact databases, submit BLAST/SRA jobs, or run molecular analyses.