Optimization of cDNA-AFLP experiments using genomic sequence data

Optimization of cDNA-AFLP experiments using genomic sequence data

MOTIVATION cDNA amplified fragment length polymorphism (cDNA-AFLP) is one of the few genome-wide level expression profiling methods capable of finding genes that have not yet been cloned or even predicted from sequence but have interesting expression patterns under the studied conditions. In cDNA-AFLP, a complex cDNA mixture is divided into small subsets using restriction enzymes and selective ...

GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP.

The release of vast quantities of DNA sequence data by large-scale genome and expressed sequence tag (EST) projects underlines the necessity for the development of efficient and inexpensive ways to link sequence databases with temporal and spatial expression profiles. Here we demonstrate the power of linking cDNA sequence data (including EST sequences) with transcript profiles revealed by cDNA-...

cDNA Microarray Data Normalization

Mining New Motifs from Cdna Sequence Data

General biological databases that store basic information on genome, transcriptome, and proteome are indispensable sequence discovery resources. However, they are not necessarily useful for inferring functions of proteins. To see this, we observe that SWISS-PROT —a protein knowledgebase containing curated protein sequences and functional information on domains and diseases—has grown a mere 26-f...

Components of variance in transcriptomics based on electrophoretic separation of cDNA fragments (cDNA-AFLP)

The sources of variance and errors in transcriptomics based on the electrophoretic separation of amplified cDNA fragments were investigated using cDNA-amplified fragment length polymorphism (AFLP). Transcriptome profiles of the plant-pathogenic fungus Verticillium longisporum were generated by a standard cDNA-AFLP protocol followed by electrophoretic separation of amplified DNA fragments in fla...