GlySeq Instructions

GlySeq is a software for a statistical analysis of the amino acid composition around glycosylation sites. The data was derived from the Protein Data Bank (PDB) using pdb2linucs or from SwissProt.

General settings:

You can choose between several different data sets: You can analyse data obtained from PDB, SwissProt or the entire data. Since for example many protein structures in the PDB consist of several chains with identical sequence or are resolved at different resolutions, there is a lot of redundancy within the "all sequences" data sets. This is eliminated in the data set "non-redundant sequences", which, of course, is smaller than the former one.

In the fields "Preceeding residues" and "Following residues" the range around the glycosylation sites to be analysed is defined.

For graphical output (SVG/GIF), the size (in pixels) can be defined.
By default, the y-axis scaling is adjusted automatically by GlySeq. Additionally, you can define the ranges above and below zero manually, e.g. to be able to easily compare results obtained from different analysis parameters.

Analysis parameters:

First of all, the glycosylation type is specified: Analysis is possible for N-glycans (Asn), O-glycan (Ser/Thr), Ser only, Thr only, or all glycans. Asp and Glu can also be chosen, but since there are very few carbohydrates attached to these residues found in the PDB, the results are not significant yet.

Next, the residues to be analysed have to be chosen. Analysis is possible for positions around the glycosylation site, e.g. the amino acid compositions at position +1 or -3, or for specified residues at the range of positions defined above. Residue are specified by their one-letter-code. Besides the 20 amino acids, the following codes are defined:
B:glycosylated Asn
O:glycosylated Ser
U:glycosylated Thr
J:glycosylated Asp
Z:glycosylated Glu
X:unknown amino acid
*:non amino acid residue
#:Position before sequence start or after sequence end
+:Distance from sequence start or sequence end
To combine several residues or positions in one query, just enter the codes of all residues to be analysed, e.g. "TSUO" for all Thr and Ser residues - glycosylated and non-glycosylated. The order of the letters has no influence on the results. Multiple positions have to be seperated by commas, e.g. "-2,-1,1,2" will analyse the amino acids at the positions from -2 to +2.

Sundry types of values are available for output:
Additionally, you can chose between three different types of output depiction: A text only mode, where the resulting values are displayed in a table, and two modes including graphics (SVG or GIF).

For refinement of the analyis, you can apply filters, that means you can specify residues, which must or must not be preset at a certain position. Using filters, you can e.g. investigate the differences between N-glycans having a Serine at position +2 and those with a Threonine at that position.

Go to the GlySeq Input Form.

In case of comments or questions please contact Thomas Lütteke.

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