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Toolboxes for a standardised and systematic study of glycans

BACKGROUND: Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time r...

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Autores principales: Campbell, Matthew P, Ranzinger, René, Lütteke, Thomas, Mariethoz, Julien, Hayes, Catherine A, Zhang, Jingyu, Akune, Yukie, Aoki-Kinoshita, Kiyoko F, Damerell, David, Carta, Giorgio, York, Will S, Haslam, Stuart M, Narimatsu, Hisashi, Rudd, Pauline M, Karlsson, Niclas G, Packer, Nicolle H, Lisacek, Frédérique
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016020/
https://www.ncbi.nlm.nih.gov/pubmed/24564482
http://dx.doi.org/10.1186/1471-2105-15-S1-S9
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author Campbell, Matthew P
Ranzinger, René
Lütteke, Thomas
Mariethoz, Julien
Hayes, Catherine A
Zhang, Jingyu
Akune, Yukie
Aoki-Kinoshita, Kiyoko F
Damerell, David
Carta, Giorgio
York, Will S
Haslam, Stuart M
Narimatsu, Hisashi
Rudd, Pauline M
Karlsson, Niclas G
Packer, Nicolle H
Lisacek, Frédérique
author_facet Campbell, Matthew P
Ranzinger, René
Lütteke, Thomas
Mariethoz, Julien
Hayes, Catherine A
Zhang, Jingyu
Akune, Yukie
Aoki-Kinoshita, Kiyoko F
Damerell, David
Carta, Giorgio
York, Will S
Haslam, Stuart M
Narimatsu, Hisashi
Rudd, Pauline M
Karlsson, Niclas G
Packer, Nicolle H
Lisacek, Frédérique
author_sort Campbell, Matthew P
collection PubMed
description BACKGROUND: Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. METHODS: Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. RESULTS: Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. CONCLUSIONS: Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.
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spelling pubmed-40160202014-05-23 Toolboxes for a standardised and systematic study of glycans Campbell, Matthew P Ranzinger, René Lütteke, Thomas Mariethoz, Julien Hayes, Catherine A Zhang, Jingyu Akune, Yukie Aoki-Kinoshita, Kiyoko F Damerell, David Carta, Giorgio York, Will S Haslam, Stuart M Narimatsu, Hisashi Rudd, Pauline M Karlsson, Niclas G Packer, Nicolle H Lisacek, Frédérique BMC Bioinformatics Research BACKGROUND: Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. METHODS: Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. RESULTS: Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. CONCLUSIONS: Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics. BioMed Central 2014-01-10 /pmc/articles/PMC4016020/ /pubmed/24564482 http://dx.doi.org/10.1186/1471-2105-15-S1-S9 Text en Copyright © 2014 Campbell et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Campbell, Matthew P
Ranzinger, René
Lütteke, Thomas
Mariethoz, Julien
Hayes, Catherine A
Zhang, Jingyu
Akune, Yukie
Aoki-Kinoshita, Kiyoko F
Damerell, David
Carta, Giorgio
York, Will S
Haslam, Stuart M
Narimatsu, Hisashi
Rudd, Pauline M
Karlsson, Niclas G
Packer, Nicolle H
Lisacek, Frédérique
Toolboxes for a standardised and systematic study of glycans
title Toolboxes for a standardised and systematic study of glycans
title_full Toolboxes for a standardised and systematic study of glycans
title_fullStr Toolboxes for a standardised and systematic study of glycans
title_full_unstemmed Toolboxes for a standardised and systematic study of glycans
title_short Toolboxes for a standardised and systematic study of glycans
title_sort toolboxes for a standardised and systematic study of glycans
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016020/
https://www.ncbi.nlm.nih.gov/pubmed/24564482
http://dx.doi.org/10.1186/1471-2105-15-S1-S9
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