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Author(s)
     X.Luo, F.Dehne, P.Liang
Title
     Identification of transposon insertion polymorphisms by computational comparative analysis of next generation personal genome data
Publication Name
     Int. Conference on Applied Mathematics, Modeling and Computational Science
Publication Type
     Proceedings
Publisher
     AIP Conf. Proc
Place
     
Editor(s)
     
Number
     
School
     
Volume
      1368
Chapter
     
Pages
      163-166
Other Publication Information
     
Publication Year
     2011
Abstract
     Structural variations (SVs) in a genome are now known as a prominent and important type of genetic variation. Among all types of SVs, the identification of transposon insertion polymorphisms (TIPs) is more challenging due to the highly repetitive nature of transposon sequences. We developed a computational method, TIP-finder, to identify TIPs through analysis of next generation personal genome data and their extremely large copy numbers. We tested the efficiency of TIP-finder with simulated data and are able to detect about 88% of TIPs with precision of >=91%. Using TIP-finder to analyze the Solexa pair-end sequence data at deep coverage for six genomes representing two trio families, we identified a total of 5569 TIPs, consisting of 4881, 456, 91, and 141 insertions from Alu, L1, SVA and HERV, respectively, representing the most comprehensive analysis of such type of genetic variation.
Keywords
     genetics, DNA, data analysis, reaction kinetics; Genomics, DNA, Data analysis: algorithms and implementation; data management, Reactions and kinetics
Website
     http://adsabs.harvard.edu/abs/2011AIPC.1368..163L
Paper Status
     Published
DOI / Publication ID
     10.1063/1.3663485



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