Compozitor queries the GlyConnect database to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarising information searched in the database.
Robin T, Mariethoz J, Lisacek F (2020)
Examining and fine-tuning the selection of glycan compositions with GlyConnect Compozitor, Mol Cell Proteomics
The following table summarises the basic constituents of glycan compositions:
|Residue type||Short name||Abbreviated code||Condensed code|
Uses the abbreviated code for residues (see table) and a semicolon as a separator between this code and the corresponding number of residues. Each such pair is separated from the next by a space. The N-glycan core is represented in this notation as: Hex:3 HexNAc:2.
Uses the abbreviated code for residues and brackets to delineate the corresponding number of residues for this code. No space separates code-number pairs. The N-glycan core is represented in this notation as: Hex(3)HexNAc(2).
Uses the condensed code (see table) immediately followed by the corresponding number of residues. No space separates code-number pairs. The N-glycan core is represented as: h2N2.
The range of user actions in the interface is illustrated in this library of GIFs:
Glycan property barplot
These nodes are computed by performing the systematic pairwise comparison of all compositions in a graph. If two compositions differ from exactly two residues, the two corresponding nodes are tentatively connected through an intermediary node that is only one residue away from each. Then, this tentative node is added only if it meets two conditions:
- It does not already exist in the graph
- None of its children has a non-virtual parent node.
The second rule avoids overcrowding the graph with multiple alternative paths. The introduction of virtual nodes increases the connectivity of a graph.
reflects the number of recorded publications supporting the corresponding composition
- The inner label reflects the number of solved structures stored in the database for the corresponding composition.
Reflects the results of up to three queries launched successively:
- A single query result is named A and displayed in a graph with blue nodes.
- A double query results are named A and B and displayed respectively in blue (A) and red (B).
- A triple query results are named A, B and C and displayed respectively in blue (A) and red (B) and green (C).
- Shared compositions between several sets of results are shown in magenta (common to A and B), yellow (common to A and C), cyan (common to B and C) and black (common to all).
The letter of the condensed notation, corresponding to the added residue.
Reflect the action of the user:
- Positioning the cursor on a node highlights entering paths in cyan and exiting paths in orange.
- Positioning the cursor on a path label highlights all paths sharing this label according to the following: