[Biopython] Are there tools for automatically parsing glycan names into tree structures?

[Nathan Edwards]

> Many apologies if you have seen this post cross-posted elsewhere. I have
> tried digging around but could not find an answer to my question.
> 
> My colleague and I are working on a project involving data produced at a
> glycan microarray facility. The array data that came back to us were a list
> of glycan names (in the format (random example from the top of my head):
> GlcNAc...). We would like to parse the list of 610 names into the graphical
> representation of the glycan.
> 
> Is this possible? If so, what tools are available to get this done?

My now graduated student (Kevin Brown-Chandler) and I have been
developing python tools for the interpretation of CID tandem
mass-spectra of N-glycopeptides for a while now, and have a reasonably
mature tool for working with these datasets.

As part of this infrastructure are python modules for parsing a variety
of (N- and O-) glycan structure description formats; glycan structure
manipulation, fragmentation, and naming (oxford notation abbreviations);
and glycan structure image generation (using the java libraries from
GlycoWorkbench). The tools for indexing glycan structure databases and
generating images from the indexed databases are distributed with the
search software, and we currently distribute a pre-indexed glycan
database of (most of) the glycans on the Consortium for Functional
Glycomics Mammalian array (v5.1).

Download GlycoPeptideSearch (GPS) here: http://grg.tn/GPS

Since it is unlikely the current tools do exactly what you need, feel
free to ping me back with more specifics, and I'll see what I can do to
help.

Cheers!

- n

-- 
Dr. Nathan Edwards                      nje5 at georgetown.edu
Department of Biochemistry and Molecular & Cellular Biology
           Georgetown University Medical Center
Room 1215, Harris Building          Room 347, Basic Science
3300 Whitehaven St, NW              3900 Reservoir Road, NW
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