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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.


Alignment of region -45, 0 and 45 with current residue, right-to-left orientation. a) If region 0 is not empty, region -45 and region 45 are aligned at right with region 0 and placed on the bottom and the top of it respectively. After that, the centre of region 0 is aligned with the centre of the current residue and the three regions are placed on the left of current residue. b) If region 0 is empty and only one region between -45 and 45 contains residues, the non-empty region is placed on the corner of the current residue, on top-left or bottom-left accordingly. c) If region 0 is empty, the regions -45 and 45 are placed on the corners of the current residue (top-left or bottom-left accordingly).
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Figure 8: Alignment of region -45, 0 and 45 with current residue, right-to-left orientation. a) If region 0 is not empty, region -45 and region 45 are aligned at right with region 0 and placed on the bottom and the top of it respectively. After that, the centre of region 0 is aligned with the centre of the current residue and the three regions are placed on the left of current residue. b) If region 0 is empty and only one region between -45 and 45 contains residues, the non-empty region is placed on the corner of the current residue, on top-left or bottom-left accordingly. c) If region 0 is empty, the regions -45 and 45 are placed on the corners of the current residue (top-left or bottom-left accordingly).

Mentions: The alignment of left regions (-45, 0, 45) with the current residue has three special cases (Figure 8). If region 0 is not empty, region -45 and region 45 are aligned at right with region 0 and placed on the bottom and the top of it respectively (Figure 8a). After that, the centre of region 0 is aligned with the centre of the current residue and the three regions are placed on the left of current residue. If region 0 is empty and only one region between -45 and 45 contains residues, the non-empty region is placed on the corner of the current residue, on top-left or bottom-left accordingly (Figure 8b). Finally, if both region -45 and 45 are non empty, they are first aligned on their rights and then placed symmetrically on the left of current residue (Figure 8c).


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)

Alignment of region -45, 0 and 45 with current residue, right-to-left orientation. a) If region 0 is not empty, region -45 and region 45 are aligned at right with region 0 and placed on the bottom and the top of it respectively. After that, the centre of region 0 is aligned with the centre of the current residue and the three regions are placed on the left of current residue. b) If region 0 is empty and only one region between -45 and 45 contains residues, the non-empty region is placed on the corner of the current residue, on top-left or bottom-left accordingly. c) If region 0 is empty, the regions -45 and 45 are placed on the corners of the current residue (top-left or bottom-left accordingly).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Alignment of region -45, 0 and 45 with current residue, right-to-left orientation. a) If region 0 is not empty, region -45 and region 45 are aligned at right with region 0 and placed on the bottom and the top of it respectively. After that, the centre of region 0 is aligned with the centre of the current residue and the three regions are placed on the left of current residue. b) If region 0 is empty and only one region between -45 and 45 contains residues, the non-empty region is placed on the corner of the current residue, on top-left or bottom-left accordingly. c) If region 0 is empty, the regions -45 and 45 are placed on the corners of the current residue (top-left or bottom-left accordingly).
Mentions: The alignment of left regions (-45, 0, 45) with the current residue has three special cases (Figure 8). If region 0 is not empty, region -45 and region 45 are aligned at right with region 0 and placed on the bottom and the top of it respectively (Figure 8a). After that, the centre of region 0 is aligned with the centre of the current residue and the three regions are placed on the left of current residue. If region 0 is empty and only one region between -45 and 45 contains residues, the non-empty region is placed on the corner of the current residue, on top-left or bottom-left accordingly (Figure 8b). Finally, if both region -45 and 45 are non empty, they are first aligned on their rights and then placed symmetrically on the left of current residue (Figure 8c).

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.