alexa A weighted q-gram method for glycan structure classification.


Journal of Glycobiology

Author(s): Li L, Ching WK, Yamaguchi T, AokiKinoshita KF

Abstract Share this page

Abstract BACKGROUND: Glycobiology pertains to the study of carbohydrate sugar chains, or glycans, in a particular cell or organism. Many computational approaches have been proposed for analyzing these complex glycan structures, which are chains of monosaccharides. The monosaccharides are linked to one another by glycosidic bonds, which can take on a variety of comformations, thus forming branches and resulting in complex tree structures. The q-gram method is one of these recent methods used to understand glycan function based on the classification of their tree structures. This q-gram method assumes that for a certain q, different q-grams share no similarity among themselves. That is, that if two structures have completely different components, then they are completely different. However, from a biological standpoint, this is not the case. In this paper, we propose a weighted q-gram method to measure the similarity among glycans by incorporating the similarity of the geometric structures, monosaccharides and glycosidic bonds among q-grams. In contrast to the traditional q-gram method, our weighted q-gram method admits similarity among q-grams for a certain q. Thus our new kernels for glycan structure were developed and then applied in SVMs to classify glycans. RESULTS: Two glycan datasets were used to compare the weighted q-gram method and the original q-gram method. The results show that the incorporation of q-gram similarity improves the classification performance for all of the important glycan classes tested. CONCLUSION: The results in this paper indicate that similarity among q-grams obtained from geometric structure, monosaccharides and glycosidic linkage contributes to the glycan function classification. This is a big step towards the understanding of glycan function based on their complex structures.
This article was published in BMC Bioinformatics and referenced in Journal of Glycobiology

Relevant Expert PPTs

Recommended Conferences

  • International Conference on Glycobiology
    Sep 21-22, 2017, Crowne Plaza Houston River Oaks, Houston, USA
  • 2nd International Conference on Biochemistry
    Sep 21-22, 2017 Macau, Hong Kong
  • International Conference on Glycobiology
    Oct 02-04, 2017 Atlanta, USA
  • 4th International Conference on Glycobiology and Glycochemistry
    July 16-18, 2018 Melbourne, Australia
  • 4th Glycobiology World Congress
    September 17-19, 2018 Rome, Italy
Peer Reviewed Journals
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

© 2008-2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version