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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.


Effect of the "sticky" attribute. This figure shows the effect of the "sticky" attribute on the placement of residues. If a position is "sticky", all the subsequent children are placed in position 0: in this way it is possible to force sub-trees in regions with a change in orientation to be drawn as a sequences (a), thus avoiding the creation of spiralling series of residues (b). The structure drawn in this figure does not represent an actual glycan.
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Figure 5: Effect of the "sticky" attribute. This figure shows the effect of the "sticky" attribute on the placement of residues. If a position is "sticky", all the subsequent children are placed in position 0: in this way it is possible to force sub-trees in regions with a change in orientation to be drawn as a sequences (a), thus avoiding the creation of spiralling series of residues (b). The structure drawn in this figure does not represent an actual glycan.

Mentions: The positioning algorithm navigates recursively from the root to the leaves of the tree structure using the set of rules in the graphical model to decide the positions of the children of each node. A positioning rule is composed by a matching operator and a set of attributes. The matching operator identifies if a rule applies to a triplet comprised by the parent residue, the child residue and the linkage. The matching operator is a Boolean function constituted of logical conditions combined using Boolean operators (and, or, negation, parenthesis). Each condition matches a certain parent, linkage or child attribute: residue type, linkage position, anomeric state, position of the anomeric carbon or residue class (e.g. saccharides, reducing ends, brackets ...). The attributes of a rule are: a set of possible positions for this residue, a flag identifying if the residue is on a border region, a flag identifying if the orientation of the child is the same as the parent or should rotate accordingly to the position angle, a flag identifying if the position is "sticky". If a position is "sticky", all the subsequent children are placed in position 0: in this way it is possible to force sub-trees in regions with a change in orientation to be drawn as a sequences, thus avoiding the creation of spiralling series of residues (Figure 5). Examples of positioning rules are:


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)

Effect of the "sticky" attribute. This figure shows the effect of the "sticky" attribute on the placement of residues. If a position is "sticky", all the subsequent children are placed in position 0: in this way it is possible to force sub-trees in regions with a change in orientation to be drawn as a sequences (a), thus avoiding the creation of spiralling series of residues (b). The structure drawn in this figure does not represent an actual glycan.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Effect of the "sticky" attribute. This figure shows the effect of the "sticky" attribute on the placement of residues. If a position is "sticky", all the subsequent children are placed in position 0: in this way it is possible to force sub-trees in regions with a change in orientation to be drawn as a sequences (a), thus avoiding the creation of spiralling series of residues (b). The structure drawn in this figure does not represent an actual glycan.
Mentions: The positioning algorithm navigates recursively from the root to the leaves of the tree structure using the set of rules in the graphical model to decide the positions of the children of each node. A positioning rule is composed by a matching operator and a set of attributes. The matching operator identifies if a rule applies to a triplet comprised by the parent residue, the child residue and the linkage. The matching operator is a Boolean function constituted of logical conditions combined using Boolean operators (and, or, negation, parenthesis). Each condition matches a certain parent, linkage or child attribute: residue type, linkage position, anomeric state, position of the anomeric carbon or residue class (e.g. saccharides, reducing ends, brackets ...). The attributes of a rule are: a set of possible positions for this residue, a flag identifying if the residue is on a border region, a flag identifying if the orientation of the child is the same as the parent or should rotate accordingly to the position angle, a flag identifying if the position is "sticky". If a position is "sticky", all the subsequent children are placed in position 0: in this way it is possible to force sub-trees in regions with a change in orientation to be drawn as a sequences, thus avoiding the creation of spiralling series of residues (Figure 5). Examples of positioning rules are:

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.