SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip.

ABSTRACT:

Background

High-density short oligonucleotide microarrays are useful tools for studying biodiversity, because they can be used to investigate both nucleotide and expression polymorphisms. However, when different strains (or species) produce different signal intensities after mRNA hybridization, it is not easy to determine whether the signal intensities were affected by nucleotide or expression polymorphisms. To overcome this difficulty, nucleotide and expression polymorphisms are currently examined separately.

Results

We have developed SNEP, a new method that allows simultaneous detection of both nucleotide and expression polymorphisms. SNEP involves a robust statistical procedure based on the idea that a nucleotide polymorphism observed at the probe level can be regarded as

SUBMITTER: Fujisawa H 

PROVIDER: S-EPMC2706822 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature