wiki:GlycanDatabaseHandling

Version 1 (modified by dbrentw, 3 years ago) (diff)

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GRITS Glycan Database Handling

GRITS supports pre-defined databases of Glycan structures stored in XML format. This document describes the basic structure and how to read and load the structures for processing within GRITS

Glycan XML Basics

GRITS Objects (plugin org.grits.toolbox.ms.annotation): 1) org.grits.toolbox.ms.annotation.structure\Database.java ("database")

Contains:

a) List of GlycanStructures (tag = "glycan")
b) name
c) description, structureCount

2) org.grits.toolbox.ms.annotation.structure\GlycanStructure.java

Contains:

a) id
b) Sequence & Sequence Format
c) Sequence in Glycoworkbench (GWB) Format
To create Glycan cartoons, you will need the GWB format. You can set this directly, or you can convert a sequence of other type to GWB sequence if you provide the "Sequence Format"

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