Eukaryotic transcriptomics in silico: optimizing cDNA-AFLP efficiency.

ABSTRACT:

Background

Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on the optimization of the cDNA-AFLP assay design are rare and have typically been taxonomically restricted. Here, we model cDNA-AFLPs on all 92 eukaryotic species for which cDNA pools are currently available, using all combinations of eight restriction enzymes standard in cDNA-AFLP screens.

Results

In silco simulations reveal that cDNA pool coverage is largely determined by the choice of individual restriction enzymes and that, through the choice of optimal enzyme combinations, coverage

SUBMITTER: Stolting KN 

PROVIDER: S-EPMC2797533 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature