IUPAC Glycan Sequence Canonicalizer

A simple web application for canonicalizing IUPAC glycan sequences using the glycowork Python package.

About

This tool provides a convenient interface to convert glycan sequences into their canonicalized IUPAC representation. Simply paste your sequences, click convert, and get standardized results instantly.

Features

• Easy-to-use web interface, with paste-in or file upload (.txt/.csv) input
• Batch processing of multiple sequences across IUPAC-extended, LinearCode, GlycoCT, WURCS, Oxford, GLYCAM, GlycoWorkBench, pGlyco, StrucGP, GlySeeker, CSDB-linear, KCF, SMILES, LINUCS, GlyConnect, and GlyTouCan formats, with multi-line GlycoCT, GlycoCT XML, and KCF records read as one sequence
• Instant conversion using the canonicalize_iupac function from glycowork
• Compositions (H5N4F1A2, Hex5HexNAc4Fuc1Neu5Ac2, HexNAc(4)Hex(5)Fuc(1)NeuAc(2), {Hex:5; HexNAc:4}, with adducts such as [M+Na]+ stripped) are detected automatically and canonicalized via canonicalize_composition into shorthand, Byonic/MSFragger, or GlycReSoft strings; all-digit codes (5421 = Hex/HexNAc/Neu5Ac/dHex) via the composition checkbox
• Optional export to SMILES (offline glycowork.motif.smiles, skipping only sequences whose residues, linkage positions, or attachment points are genuinely undefined), GlycoCT, WURCS (as GlyTouCan writes it, for registration or lookup), IUPAC-extended, GLYCAM, and Oxford, plus elemental formula and monoisotopic mass for any sample preparation (underivatized, permethylated, deuteropermethylated, peracetylated) and reducing end (free, reduced with NaBH4 or NaBD4, 2-AA, 2-AB, procainamide, PA, APTS, aminoxyTMT, Girard's P, benzyl glycoside)
• SNFG rendering of structures and compositions with GlycoDraw, with optional drop shadow or sticker style, downloadable as a PDF archive; on a dark theme, the drawings on the page are die-cut stickers
• Downloadable canonicalized sequences (.txt) and conversion tables (.csv)
• Error handling for invalid sequences, a warning for text that was not recognized as a glycan, plus a built-in GitHub issue reporter

Usage

1. Enter one or more glycan sequences in the input text area (one per line)
2. Click the "Convert" button
3. View and copy the canonicalized sequences from the output area

Local Development

To run this application locally:

pip install -r requirements.txt
streamlit run app.py

Deployment

This application is deployed on Streamlit Cloud and is freely accessible at the canonicalize app.

Dependencies

• streamlit
• glycowork

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contact

For questions or issues related to this application, please open an issue on this repository. For questions about the glycowork package, visit the glycowork repository.