Accurate single individual haplotyping based on HuRef dataset using HapSAT algorithm
by Ehsan Haghshenas; Nadia Barjaste; Sayyed Rasoul Mousavi
International Journal of Functional Informatics and Personalised Medicine (IJFIPM), Vol. 4, No. 3/4, 2014

Abstract: Studying haplotypes is an important approach for investigation of genetic variations in the human genome because they contain a lot of information related to these types of variations. The haplotype assembly problem is to reconstruct two haplotypes for an individual using a set of aligned single nucleotide polymorphism (SNP) fragments from the two haplotypes (related to a particular chromosome). This problem is recognised as an NP-hard problem due to possible sequencing errors. Therefore, in practice, heuristic algorithms are used for finding satisfactory solutions to this problem. In this paper, an optimised reimplementation of HapSAT algorithm has been used to find haplotypes for HuRef dataset. Finding more accurate haplotypes based on this dataset is of considerable importance, because HuRef haplotypes are widely used in some researches (in biology, medicine, and pharmacy). Since the HapSAT algorithm provides significantly superior results compared to previously proposed algorithms, assembled haplotypes using HapSAT algorithm will be very useful for future researches.

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