AtRTPrimer

Abstract

Quantitative RT-PCR methods are usually being used to overcome drawbacks of microarray technology caused by variability and detection of low expression level. Primer design is very critical step in RT-PCR methods to guarantee specificity and efficiency of a target amplicon. However, most of traditional primer design programs suggest primers on a single template of limited genetic complexity. In online RT-PCR primer databases, they contain the validated primers for small fraction of whole genes at present. To provide researchers with enough specific RT-PCR primer pairs for whole genes in Arabidopsis, we constructed and evaluated genome-wide primer-pairs database, which is called AtRTPrimer, considering homogeneous physical and chemical properties of each primer (homogeneity) of a gene, non-specific binding against all known genes (specificity), and another possible amplicons from its corresponding genomic DNA or similar cDNA (noise). This database is designed for a couple of types of quantitative RT-PCR: roughly speaking, conventional RT-PCR and real-time RT-PCR. Therefore, experimentalists can find out the appropriate set of pre-designed primer-pairs of their target genes to perform the desired type of RT-PCR using filtering conditions.