Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

K.N. Stölting, G. Gort, C. Wüst, A.B. Wilson

Research output: Contribution to journalArticleAcademicpeer-review

10 Citations (Scopus)

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 can be increased from
Original languageEnglish
Article number565
Number of pages15
JournalBMC Genomics
Volume10
DOIs
Publication statusPublished - 2009

Keywords

  • full-length cdnas
  • differential gene-expression
  • identification
  • distributions
  • resistance
  • sequences
  • resources
  • markers
  • library
  • plant

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