glycoprotein alignment

GlycoSiteAlign

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GlycoSiteAlign selectively aligns amino acid sequences surrounding glycosylation sites (by default, 20 positions on each side of the glycosylated residue) depending on structural properties of the glycan attached to the site. These properties are either general (e.g., "fucosylated") or specific, such as precise composition, and are proposed in a drop-down list.

This tool was designed upon observing that the similarity of glycan structures (shared properties) impacts on the regularity of site alignment. The knowledge of structural details at specificied sites is extracted from GlyConnect (https://glyconnect.expasy.org/).

Due to currently limited knowledge of glycan structures at specific sites, the more specific the glycan properties, the fewer amino acid sequences can be aligned. To compensate for this lack of data GlycoSiteAlign offers the option of fetching homologous proteins in UniProt as suggested in the "90% similar proteins" section of each selected glycoprotein entry. A box can be ticked to validate this option.

Alignment/s is/are returned as text file/s, svg image/s and when available, the 3D structure of the glycosites can be visualized through Mol*.

For further details on GlycoSiteAlign please refer to this publication: "GlycoSiteAlign: Glycosite alignment based on glycan structure"

COBALT, a constraint-based alignment tool, is used to do the alignments: bioinformatics.oxfordjournals.org/content/23/9/1073
Jalview is used to visualise the alignments as svg images: bioinformatics.oxfordjournals.org/content/25/9/1189
UniProt release date: 28-February-2018
GlycoSiteAlign last update date: 28-February-2018

Glycosylation site alignment

Search for glycans and align glycosylation sites