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bioRxiv · 10.1101/2024.02.01.578383

Syntactic Sugars: Crafting a Regular Expression Framework for Glycan Structures

Bennett, A. R.·Bojar, D.
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Abstract

SummaryStructural analysis of glycans pose significant challenges in glycobiology due to their complex sequences. Research questions such as analyzing the sequence content of the 1-6 branch in N- glycans, are biologically meaningful yet can be hard to automate. Here, we introduce a regular expression system, designed for glycans, feature-complete, and closely aligned with regular expression formatting. We use this to annotate glycan motifs of arbitrary complexity, perform differential expression analysis on designated sequence stretches, or elucidate branch-specific binding specificities of lectins in an automated manner. We are confident that glycan regular expressions will empower computational analyses of these sequences. Availability and implementationOur regular expression framework for glycans is implemented in Python and is incorporated into the open-source glycowork package (version 1.1+). Code and documentation are available at https://github.com/BojarLab/glycowork/blob/master/glycowork/motif/regex.py. Contactdaniel.bojar@gu.se

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Bennett, A. R., Bojar, D.. 2024-02-02. Syntactic Sugars: Crafting a Regular Expression Framework for Glycan Structures. https://doi.org/10.1101/2024.02.01.578383

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