A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees | Zendy

Mark Silberstein | Zendy; Omer Weissbrod | Zendy; Lars Otten | Zendy; Anna Tzemach | Zendy; Andrei Anisenia | Zendy; Oren Shtark | Zendy; Dvir Tuberg | Zendy; Eddie Galfrin | Zendy; Irena Gan | Zendy; Adel Shalata | Zendy; Zvi Borochowitz | Zendy; Rina Dechter | Zendy; E. A. Thompson | Zendy; Dan Geiger | Zendy

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A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees

Author(s) -

Mark Silberstein,

Omer Weissbrod,

Lars Otten,

Anna Tzemach,

Andrei Anisenia,

Oren Shtark,

Dvir Tuberg,

Eddie Galfrin,

Irena Gan,

Adel Shalata,

Zvi Borochowitz,

Rina Dechter,

E. A. Thompson,

Dan Geiger

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts658

Subject(s) - tag snp , computer science , snp , markov chain monte carlo , workflow , linkage (software) , data mining , pedigree chart , theoretical computer science , haplotype , single nucleotide polymorphism , bayesian probability , genetics , artificial intelligence , database , biology , gene , genotype

The use of dense single nucleotide polymorphism (SNP) data in genetic linkage analysis of large pedigrees is impeded by significant technical, methodological and computational challenges. Here we describe Superlink-Online SNP, a new powerful online system that streamlines the linkage analysis of SNP data. It features a fully integrated flexible processing workflow comprising both well-known and novel data analysis tools, including SNP clustering, erroneous data filtering, exact and approximate LOD calculations and maximum-likelihood haplotyping. The system draws its power from thousands of CPUs, performing data analysis tasks orders of magnitude faster than a single computer. By providing an intuitive interface to sophisticated state-of-the-art analysis tools coupled with high computing capacity, Superlink-Online SNP helps geneticists unleash the potential of SNP data for detecting disease genes.

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