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The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures.

Ceroni A, Dell A, Haslam SM - Source Code Biol Med (2007)

Bottom Line: However, the additional complexity of glycans compared to proteins and nucleic acids has slowed the advancement of glycomics in comparison to genomics and proteomics.Every glycoinformatic tool providing a user interface would benefit from a fast, intuitive, appealing mechanism for input and output of glycan structures in a computer readable format.The "GlycanBuilder" represent a flexible, reliable and efficient solution to the problem of input and output of glycan structures in any glycomic tool or database.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Molecular Biosciences, Imperial College London, SW7 2AZ, UK. a.ceroni@imperial.ac.uk.

ABSTRACT

Background: Carbohydrates play a critical role in human diseases and their potential utility as biomarkers for pathological conditions is a major driver for characterization of the glycome. However, the additional complexity of glycans compared to proteins and nucleic acids has slowed the advancement of glycomics in comparison to genomics and proteomics. The branched nature of carbohydrates, the great diversity of their constituents and the numerous alternative symbolic notations, make the input and display of glycans not as straightforward as for example the amino-acid sequence of a protein. Every glycoinformatic tool providing a user interface would benefit from a fast, intuitive, appealing mechanism for input and output of glycan structures in a computer readable format.

Results: A software tool for building and displaying glycan structures using a chosen symbolic notation is described here. The "GlycanBuilder" uses an automatic rendering algorithm to draw the saccharide symbols and to place them on the drawing board. The information about the symbolic notation is derived from a configurable graphical model as a set of rules governing the aspect and placement of residues and linkages. The algorithm is able to represent a structure using only few traversals of the tree and is inherently fast. The tool uses an XML format for import and export of encoded structures.

Conclusion: The rendering algorithm described here is able to produce high-quality representations of glycan structures in a chosen symbolic notation. The automated rendering process enables the "GlycanBuilder" to be used both as a user-independent component for displaying glycans and as an easy-to-use drawing tool. The "GlycanBuilder" can be integrated in web pages as a Java applet for the visual editing of glycans. The same component is available as a web service to render an encoded structure into a graphical format. Finally, the "GlycanBuilder" can be integrated into other applications to create intuitive and appealing user interfaces: an example is the "GlycoWorkbench", a software tool for assisted annotation of glycan mass spectra. The "GlycanBuilder" represent a flexible, reliable and efficient solution to the problem of input and output of glycan structures in any glycomic tool or database.

No MeSH data available.


Orientation and style of linkages in UOXF notation. In the symbolic notation adopted by the Oxford Glycobiology Institute the anomeric state is represented by varying the style of the line (dashed or continuous) while the linkage position is represented by the orientation of the saccharide in respect to its parent.
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Figure 2: Orientation and style of linkages in UOXF notation. In the symbolic notation adopted by the Oxford Glycobiology Institute the anomeric state is represented by varying the style of the line (dashed or continuous) while the linkage position is represented by the orientation of the saccharide in respect to its parent.

Mentions: A second proposal for representing linkage information, originally suggested in [18], has been adopted by the Oxford Glycobiology Institute (UOXF) and is detailed in [19]. In this notation, the anomeric state is represented by varying the style of the line (dashed or continuous) while the linkage position is visually represented by the orientation of the saccharide in respect of its parent (Figure 2). A curved line is used for the linkage if the position is unknown. The symbols used for saccharides are all in black and white and are limited when compared to those used by the CFG (Figure 1). A mixed notation using CFG symbols and UOXF linkage notation has also been proposed. Example of a structure depicted with CFG and UOXF notations is given in Figure 3.


The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures.

Ceroni A, Dell A, Haslam SM - Source Code Biol Med (2007)

Orientation and style of linkages in UOXF notation. In the symbolic notation adopted by the Oxford Glycobiology Institute the anomeric state is represented by varying the style of the line (dashed or continuous) while the linkage position is represented by the orientation of the saccharide in respect to its parent.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1994674&req=5

Figure 2: Orientation and style of linkages in UOXF notation. In the symbolic notation adopted by the Oxford Glycobiology Institute the anomeric state is represented by varying the style of the line (dashed or continuous) while the linkage position is represented by the orientation of the saccharide in respect to its parent.
Mentions: A second proposal for representing linkage information, originally suggested in [18], has been adopted by the Oxford Glycobiology Institute (UOXF) and is detailed in [19]. In this notation, the anomeric state is represented by varying the style of the line (dashed or continuous) while the linkage position is visually represented by the orientation of the saccharide in respect of its parent (Figure 2). A curved line is used for the linkage if the position is unknown. The symbols used for saccharides are all in black and white and are limited when compared to those used by the CFG (Figure 1). A mixed notation using CFG symbols and UOXF linkage notation has also been proposed. Example of a structure depicted with CFG and UOXF notations is given in Figure 3.

Bottom Line: However, the additional complexity of glycans compared to proteins and nucleic acids has slowed the advancement of glycomics in comparison to genomics and proteomics.Every glycoinformatic tool providing a user interface would benefit from a fast, intuitive, appealing mechanism for input and output of glycan structures in a computer readable format.The "GlycanBuilder" represent a flexible, reliable and efficient solution to the problem of input and output of glycan structures in any glycomic tool or database.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Molecular Biosciences, Imperial College London, SW7 2AZ, UK. a.ceroni@imperial.ac.uk.

ABSTRACT

Background: Carbohydrates play a critical role in human diseases and their potential utility as biomarkers for pathological conditions is a major driver for characterization of the glycome. However, the additional complexity of glycans compared to proteins and nucleic acids has slowed the advancement of glycomics in comparison to genomics and proteomics. The branched nature of carbohydrates, the great diversity of their constituents and the numerous alternative symbolic notations, make the input and display of glycans not as straightforward as for example the amino-acid sequence of a protein. Every glycoinformatic tool providing a user interface would benefit from a fast, intuitive, appealing mechanism for input and output of glycan structures in a computer readable format.

Results: A software tool for building and displaying glycan structures using a chosen symbolic notation is described here. The "GlycanBuilder" uses an automatic rendering algorithm to draw the saccharide symbols and to place them on the drawing board. The information about the symbolic notation is derived from a configurable graphical model as a set of rules governing the aspect and placement of residues and linkages. The algorithm is able to represent a structure using only few traversals of the tree and is inherently fast. The tool uses an XML format for import and export of encoded structures.

Conclusion: The rendering algorithm described here is able to produce high-quality representations of glycan structures in a chosen symbolic notation. The automated rendering process enables the "GlycanBuilder" to be used both as a user-independent component for displaying glycans and as an easy-to-use drawing tool. The "GlycanBuilder" can be integrated in web pages as a Java applet for the visual editing of glycans. The same component is available as a web service to render an encoded structure into a graphical format. Finally, the "GlycanBuilder" can be integrated into other applications to create intuitive and appealing user interfaces: an example is the "GlycoWorkbench", a software tool for assisted annotation of glycan mass spectra. The "GlycanBuilder" represent a flexible, reliable and efficient solution to the problem of input and output of glycan structures in any glycomic tool or database.

No MeSH data available.