Enzyme classification using reactive motifs
by Thanapat Kangkachit; Kitsana Waiyamai; Philippe Lenca
International Journal of Functional Informatics and Personalised Medicine (IJFIPM), Vol. 4, No. 3/4, 2014

Abstract: Reactive motifs are short conserved sub-sequences discovered from functional sites of enzyme sequences, and can be used as an effective representation of enzyme sequences. However, the lack of site information leads to low-coverage reactive motifs. With the use of background knowledge, a motif generalisation method is required to increase reactive motifs' coverage. We show that a fuzzy concept lattice (FCL) provides an efficient representation of both single-value and multi-value biological background knowledge and an efficient computational support for generalising reactive motifs. Compared to statistical and expert-based motifs, we show that the generalised reactive motifs using FCL with SVM classifier produce satisfactory accuracy in classifying new enzymes. Further, they improve interpretability of the classification results and provide more biological evidences to biologists. All of the generalised reactive motifs are relevant to the functional sites, and the way they are combined to perform protein function is useful for numerous applications in bioinformatics.

Online publication date: Sun, 22-Mar-2015

The full text of this article is only available to individual subscribers or to users at subscribing institutions.

Existing subscribers:
Go to Inderscience Online Journals to access the Full Text of this article.

Pay per view:
If you are not a subscriber and you just want to read the full contents of this article, buy online access here.

Complimentary Subscribers, Editors or Members of the Editorial Board of the International Journal of Functional Informatics and Personalised Medicine (IJFIPM):
Login with your Inderscience username and password:

    Username:        Password:         

Forgotten your password?

Want to subscribe?
A subscription gives you complete access to all articles in the current issue, as well as to all articles in the previous three years (where applicable). See our Orders page to subscribe.

If you still need assistance, please email subs@inderscience.com