CloudTSS: A TagSNP selection approach on cloud computing

Che Lun Hung*, Yaw Ling Lin, Guan Jie Hua, Yu Chen Hu

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

6 Scopus citations

Abstract

SNPs are fundamental roles for various applications including medical diagnostic, phylogenies and drug design. They provide the highest-resolution genetic fingerprint for identifying disease associations and human features. Genetic variants that are near each other tend to be inherited together; these regions of linked variants are known as haplotypes. Recently, genetics researches revealed that SNPs within certain haplotype blocks induce only a few distinct common haplotypes in the majority of the population. The existence of haplotype block structure has serious implications for association-based methods for the mapping of disease genes. This paper proposes a parallel haplotype block partition and SNPs selection method under a diversity function by using the Hadoop MapReduce framework. The experiment shows that the proposed MapReduce-paralleled combinatorial algorithm performs well on the real-world data obtained in from the HapMap data set; the computation efficiency can be significantly improved proportional to the number of processors being used.

Original languageEnglish
Title of host publicationGrid and Distributed Computing - International Conference, GDC 2011, Held as Part of the Future Generation Information Technology Conference, FGIT 2011, Proceedings
Pages525-534
Number of pages10
DOIs
StatePublished - 2011
Externally publishedYes
EventInternational Conference on Grid and Distributed Computing, GDC 2011, Held as Part of the 3rd International Mega-Conference on Future-Generation Information Technology, FGIT 2011 - Jeju Island, Korea, Republic of
Duration: 08 12 201110 12 2011

Publication series

NameCommunications in Computer and Information Science
Volume261 CCIS
ISSN (Print)1865-0929

Conference

ConferenceInternational Conference on Grid and Distributed Computing, GDC 2011, Held as Part of the 3rd International Mega-Conference on Future-Generation Information Technology, FGIT 2011
Country/TerritoryKorea, Republic of
CityJeju Island
Period08/12/1110/12/11

Keywords

  • Hadoop
  • Haplotype
  • MapReduce
  • SNPs
  • cloud computing

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