Are There Tools For Automatically Parsing Glycan Names Into Tree Structures?

Question

[ericmajinglong]

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?

Thank you!

Answer 1

[Mary]

There might be something at the Functional Glycomics Gateway to help you. I'm not entirely sure with what you have, but have a look at what they offer: http://openhelix.com/cgi/tutorialInfo.cgi?id=123 is the training suite that covers some of the tools they provide.

At the CFG site, try this: http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/searchByLinearCode.jsp

If what you have are the IUPAC codes, you can put them in here. You get a popup window with the graphic if you click the name in the results list. Or you can click the "display cartoon images" to get those right in the results list.

I don't think there's a way to automate this query, but you could ask them.