GLYCODER

Structure-Guided DNA Barcode Design for Glycan Libraries

About GLYCODER

This tool provides bidirectional conversion between IUPAC-condensed glycans and sequencing-compatible DNA barcodes for DNA-encoded glycan libraries (DEGLs).

GLYCODER supports selectable fixed-length encoding modes, including compact modes for demonstration and high-fidelity modes with error detection or 1-bp active correction. For experimental barcode design, the 7nt high-fidelity mode is recommended.

DEGL Encoding Control Panel

Examples: Sialyl Lewis X Lewis Y N-Glycan Core LacNAc Complex N-Glycan
IUPAC Format Support: Glycan monomers, linkages, modifications and brackets are separated by " : ". Supports both custom ":" format and standard IUPAC-condensed format.

Result:

Input Glycan:
DNA Code:
Header Tag:
Total Length:
Mode Used:
IUPAC Format:

Decode DNA to Glycan (Auto-detect Header)

Automatically detects encoding mode from Header tag. Supports Max Density Mode sequences without Header.
Enter Nucleotide:
Examples (Legacy): AAGAATAATAGATAAAGA Lewis Y (Legacy)

Result:

Input DNA:
Detected Mode:
Decoded Glycan:
IUPAC Format:

Current Codebook Reference

View the complete mapping of DNA barcodes to Glycan IUPAC codes for the currently selected encoding mode.
Note: Changing the token length or mode will dynamically regenerate this table.

Methodology: DEGL Encoding Modes

Table 1: Characteristics and constraints of the encoding modes available in the DEGL system.
Encoding Mode Token Length Theoretical Capacity Error Correction Capability GC Constraints Palindrome Check
Max Density
(Legacy)		 Variable Dependent on dictionary Heuristic matching (d=N/A) None Off
Optimized
(Ultra-compact)		 4 nt ~256 tokens None (d=1) 0-100% (No limits) Off
Optimized
(Balanced / Default)		 5 nt ~996 tokens None (d=1) 0-100% (No limits) Off
Optimized
(Thermodynamic)		 6 nt >500 tokens Error detection only (d=2) 40-60% On
Optimized
(High Fidelity)		 7 nt ~350 tokens 1-bp active correction (d=3) 40-60% On

Table 1 Notes:

  • Token Length: The number of nucleotides (nt) assigned to each glycan building block or macro-compressed core.
  • Error Correction Capability: The minimum Hamming distance (d) enforced across the codebook. A distance of d=2 allows for the detection of sequencing errors, while d=3 enables the active mathematical correction of a 1-bp mutation.
  • GC Content & Palindrome: Strict thermal stability controls required for optimal PCR amplification and the prevention of polymerase slippage during library construction.

Version and Citation:

GLYCODER v1.0 manuscript version. Static codebook reference files are provided with this site as table-4nt.txt, table-5nt.txt, table-6nt.txt, table-7nt.txt, and table-max-density.txt.

If you use GLYCODER, please cite the associated manuscript: "Modular DNA-Encoded Glycan Libraries Enable Scalable, Low-Input Profiling of Glycan-Protein Interactions."

Repository: https://gitee.com/zhangc6/glycoder

License: Code is licensed under Apache-2.0. Documentation, examples, and codebook tables are licensed under CC BY 4.0 unless otherwise noted.