Export declared proteins and translation-memory pairs
Select declared CDS translations and exact TMX locale pairs with complete original files, feature or variant reports, explicit encodings and bounded downloads.
Start with the receiving task
GenBank selection answers a specific request: find CDS features whose NRPS_PKS values contain PKS_ and export the protein translations already declared there, with LOCUS, CDS IDs and locations in the headers. TMX selection answers a different request: turn an explicitly chosen source and target locale into aligned TSV text without losing the rest of the translation memory.
Select one complete local file or paste supported UTF-8 text. A selected file takes precedence. GenBank requires fatal UTF-8; TMX raw files also support UTF-16LE/BE with BOM and a matching XML1.0 declaration. File extensions do not determine the parser. Neither task sends file bytes, executes embedded content or loads external references.
| Task | Derived export | Source and complete report |
|---|---|---|
| Declared CDS proteins | proteins.faa, only unique existing translation declarations | original.gb, report.json, complete CDS report.csv |
| Explicit TMX language pair | pairs.tsv, unique paired derived text and every TU status | original.tmx, report.json with every variant and mixed-content node |
GenBank: keep the difference between match and protein
Set an ASCII qualifier key and a case-sensitive literal contains/equals value. A CDS with no such key is missing-qualifier; one with values but no match is no-match. A match with no translation is missing-translation, one empty declaration is empty-translation, and any repeated translation declarations are ambiguous-translation. Even an empty declaration plus one nonempty declaration is not automatically resolved.
Only exactly one nonempty translation declaration yields FASTA. Existing translation whitespace is removed and its declared ASCII letters/* are retained; DNA is never translated again. The header reversibly encodes record/feature indices, LOCUS, the complete ordered ID list and the declared location. Duplicate LOCUS or IDs therefore do not collide.
Fixed FEATURES columns, ordered qualifier repetition, flags, quoted values and UTF-8 byte spans remain in JSON. join/complement/fuzzy/remote locations are strings; ORIGIN/CONTIG content, declared DNA length, other headers, codons, translation tables and biological validity remain unreviewed. This is a finite nucleic GenBank profile rather than a full INSDC validator.
TMX: preserve all alternatives before taking a pair
Locale matching is exact and case-sensitive: EN-GB does not match en-gb. One source and one target variant form a pair; repeated selected variants are ambiguous, and missing source, target or both get explicit statuses. TSV paired text stays blank in those cases while the complete JSON retains all alternatives.
The declared inline profile retains bpt/ept pair identities, ph/it code data, hi/sub text, notes, properties, attributes and ordered mixed text/comments. Derived TSV excludes native code data but includes translatable hi/sub content. It cannot replace the inline-coded source. UDE mappings stay in the report but are not applied.
Only literal SYSTEM tmx14.dtd is allowed and it is never loaded. Other DTDs, entity declarations, processing instructions, ut and custom elements are Unsupported. Unknown attributes are preserved without a validity claim. XML1.0 normalization applies to JSON strings; original.tmx retains exact bytes. The tool does not certify TMX Level2 compliance or translate text.
Use the complete files when preview stops
Budgets apply together. A source within its input cap can still produce excessive complete output; the entire operation then rejects without partial downloads. Browser memory contains active source and result buffers. Cancel processing and rerun the same complete file after checking the selected controls.
| Task | Input and structural limits | Complete combined output |
|---|---|---|
| GenBank | 10MiB;10,000 records;100,000 features;20,000 matched CDS;8million declared translation characters;300,000 physical lines | 40MiB original+JSON+CSV+FASTA |
| GenBank field limits | 65,536 UTF-16 units per physical line/location;100,000 qualifiers per feature;1,048,576 ordinary qualifier units;key128;literal4,096 | Input/output total limits constrain combinations |
| TMX | 2MiB;2,000 TU;10,000 TUV;30,000 element nodes;depth64;locale64 UTF-16 units | 10MiB original+JSON+TSV |
- The table shows at most200 rows and2,000 UTF-16 units per long cell plus an ellipsis.
- Above20,000 UTF-16 units, text and clipboard contain a compact report preview; download report.json for every record and node.
- Formula-like CSV/TSV cells receive a leading apostrophe. Underlying declarations remain unchanged in JSON and original files.
- Keep original bytes when using a reported source span; GenBank BOM/CRLF and TMX UTF-16 cannot be reconstructed by guessing from normalized text.
Verify the actual handoff
For GenBank, trace each selected CDS to the original qualifier byte spans, compare its status with all translation declarations and decode the reversible FASTA header. For TMX, compare TU ordering, each locale alternative, inline pairs and metadata against the original, then use TSV only for the declared derived-text task.
The cited author files were unavailable or incomplete excerpts. Starter files are complete synthetic task reconstructions with test sequences/sentences; they are not the authors’ original scientific or translation evidence. Mature-reader and Node Worker checks are implementation evidence. Production-browser interactions and final acceptance are separate central review records.
References
- GenBank author task
First-person demand for qualifier-selected existing protein declarations; complete author file unavailable.
- TMX author task
First-person UTF16LE English/Spanish TSV task; excerpt lacks final closures; starter is synthetic.
- GenBank sample record
Field-meaning correctness reference, not demand or full INSDC validation.
- TMX1.4b specification
Correctness reference for encoding and mixed inline content; this tool claims only its declared finite profile.
Tools in this category
Expand a tool to see its steps, options and supported formats, then open its workspace.
GenBank CDS declared-protein exportSelect CDS features by a literal qualifier value and export their unique declared translations, retaining all feature statuses, qualifiers and original byte spans.
Read existing protein declarations from a complete GenBank file. Missing, empty and repeated translations remain visible; the tool does not recompute proteins from DNA.
Steps
- Select a complete GenBank file or paste UTF-8 text. Set the qualifier key, literal value and contains/equals choice.
- Inspect matched and exported counts, then check each unavailable CDS status instead of assuming every match has a protein.
- Download proteins.faa with the complete report and original.gb; preserve the source when handing off declared locations.
Available options
- Qualifier key
- NRPS_PKS
- Literal value, case-sensitive
- PKS_
- Literal matching rule
- Contains literal · Equals literal
Capabilities and limits
- One UTF-8 nucleic GenBank, optional BOM and LF/CRLF, up to10MiB. Up to10,000 records,100,000 features,20,000 matched CDS,8,000,000 declared translation ASCII characters across all features and300,000 physical lines. Complete original, JSON, CSV and FASTA together must fit40MiB.
- Physical lines and declared locations each allow65,536 UTF-16 units; up to100,000 qualifiers per feature; each ordinary decoded qualifier up to1,048,576 UTF-16 units. Selection key is an ASCII identifier up to128 units; literal selection up to4,096. Limits apply together; input and output caps constrain simultaneous maxima.
- Recognizes the nucleic LOCUS prefix, exact fixed ASCII FEATURES columns and complete ORIGIN/CONTIG plus // structure. It does not validate full INSDC headers, nucleotide content/length, locations, codons, translation tables, biology or external references. Protein LOCUS, lone CR, invalid UTF-8, unsupported indentation and translation characters are rejected.
- Contains/equals selection is literal and case-sensitive, without regular expressions. Missing qualifier and no match are distinct. Only exactly one nonempty translation declaration exports; no declaration is missing, one empty declaration is empty, and any repeated declaration is ambiguous even if one is empty.
- Full JSON preserves every parsed record/feature, ordered repeated qualifiers and flags, quote form, declared location and exact UTF-8 source spans. FASTA headers reversibly include record/feature indices, LOCUS, all ID values and location. Only whitespace is removed from existing translation values; no biological validity is inferred.
- CSV includes every CDS status and protects formula-like text with a leading apostrophe; JSON keeps the underlying value. Preview shows first200 rows and first2,000 UTF-16 units per long cell. Above20,000 units, copy is a report preview; all downloads remain complete. Originals retain BOM and LF/CRLF byte for byte.
TMX language-pair and variant exportExport explicitly selected TMX language pairs to TSV while preserving all alternatives, metadata and mixed inline content in a complete report and exact original.
Inspect the full translation memory before choosing a unique pair. Exact locale selection avoids silent fallback; missing and repeated variants remain visible rather than being guessed.
Steps
- Choose a complete TMX file or paste UTF-8 XML. Set the exact source and target locale names.
- Run the export and inspect paired, ambiguous and missing unit counts; review all alternatives in the complete report.
- Download pairs.tsv, report.json and original.tmx together. Use TSV for derived text, not as a replacement for native inline codes.
Available options
- Exact source locale
- EN-GB
- Exact target locale
- ES-ES
Capabilities and limits
- One TMX1.4 file up to2MiB, up to2,000 translation units,10,000 language variants,30,000 XML element nodes and XML depth64. Explicit locale names each allow64 UTF-16 units. Complete original, JSON and TSV together must fit10MiB; all limits apply together.
- Files are recognized from their content, not extension. Fatal UTF-8 or UTF-16LE/BE with BOM and a matching XML1.0 encoding declaration are supported. Paste is UTF-8 text. A UTF-16 file is kept as raw bytes until its parser decodes it; invalid Unicode and encoding conflicts fail atomically.
- Source and target locale names are exact and case-sensitive, with no fallback or canonicalization. Only one source and one target variant yield text. Repeated locale variants are ambiguous; missing source, target or both stay visible with blank paired text. All alternatives remain in full JSON.
- Supports declared tmx/header/body/tu/tuv/seg/note/prop/ude/map containers and bpt/ept/it/ph/hi/sub inline profile. Derived text excludes native code data and includes hi/sub translatable text. Complete node order, attributes, mixed text/comments and paired bpt/ept remain in JSON. UDE mappings are retained but not applied.
- The exact literal SYSTEM tmx14.dtd is retained without loading it. Other DTDs, entity declarations, processing instructions, ut and custom elements are Unsupported. This is not DTD validation, TMX Level2 compliance, machine translation or validation of unknown attributes. XML1.0 text/attribute normalization applies to JSON; exact original bytes remain downloadable.
- TSV contains every TU status and protects formula-like cells with an apostrophe; retain JSON/original for unmodified values and code data. Table preview is first200 rows and2,000 UTF-16 units per long cell. Above20,000 units, copied text is a report preview; complete downloads retain every node, variant and pair.