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Bioinformatics Advance Access published online on December 7, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti193
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received July 8, 2004
Revised November 24, 2004
Accepted November 27, 2004

Article

A score matrix to reveal the hidden links in glycans

Kiyoko F. Aoki 1, Hiroshi Mamitsuka 1*, Tatsuya Akutsu 1, and Minoru Kanehisa 1

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

* To whom correspondence should be addressed.
Hiroshi Mamitsuka, E-mail: mami{at}kuicr.kyoto-u.ac.jp


  Abstract

Motivation: Glycans are the third major class of biomolecules following DNA and proteins. They are extremely vital for the functioning of multi-cellular organisms. However, considering 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 verify the effectiveness of our new glycan score matrix by illustrating how the resulting score matrix entries correspond well 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.

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


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