Skip Navigation


Bioinformatics Advance Access originally published online on December 7, 2004
Bioinformatics 2005 21(8):1457-1463; doi:10.1093/bioinformatics/bti193
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/8/1457    most recent
bti193v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (12)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Aoki, K. F.
Right arrow Articles by Kanehisa, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Aoki, K. F.
Right arrow Articles by Kanehisa, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

A score matrix to reveal the hidden links in glycans

Kiyoko F. Aoki , Hiroshi Mamitsuka *, Tatsuya Akutsu and Minoru Kanehisa

Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan

*To whom correspondence should be addressed.

Motivation: Glycans are the third major class of biomolecules following DNA and proteins. They are extremely vital for the functioning of multicellular organisms. However, comparing the fast development of sequence analysis techniques, informatics work on glycans have a long way to go. Alignment algorithms for glycan tree structures are one of the foremost concerns. In addition, the statistical analysis of these algorithms in terms of biological significance needs to be addressed.

Results: We developed a tree-structure alignment algorithm for glycans and performed a statistical analysis of these alignment scores such that biologically interesting features could be captured into a score matrix for glycans. We generated our score matrix in a manner similar to BLOSUM, but with slight variations to accomodate our glycan data, including the incorporation of linkage information. We verified the effectiveness of our new glycan score matrix by illustrating how well the resulting score matrix entries correspond with biological knowledge. Future work for even better improvements with the use of a variety of score matrices for different subclasses of glycans due to their complexity is also discussed.

Contact: mami{at}kuicr.kyoto-u.ac.jp

Supplementary information: The glycan score matrix can be downloaded from http://kanehisa.kuicr.kyoto-u.ac.jp/Paper/kcam/glycanMatrix0.1.txt


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
Y. Yamanishi, F. Bach, and J.-P. Vert
Glycan classification with tree kernels
Bioinformatics, May 15, 2007; 23(10): 1211 - 1216.
[Abstract] [Full Text] [PDF]

Home page
 GlycobiologyHome page
K. Hashimoto, S. Goto, S. Kawano, K. F. Aoki-Kinoshita, N. Ueda, M. Hamajima, T. Kawasaki, and M. Kanehisa
KEGG as a glycome informatics resource
Glycobiology, May 1, 2006; 16(5): 63R - 70R.
[Abstract] [Full Text] [PDF]

Home page
 GlycobiologyHome page
T. Lutteke, A. Bohne-Lang, A. Loss, T. Goetz, M. Frank, and C.-W. von der Lieth
GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research
Glycobiology, May 1, 2006; 16(5): 71R - 81R.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.