The success of the polymerase chain reaction (PCR) is highly dependent on primer design. Commonly used primer design programs rely upon a core set of parameters such as melting temperature, primer length, GC content, and complementarity to optimize the PCR product, but weight those parameters to differing degrees, as well as include other parameters for PCR specific tasks. An analysis of these ...

UNLABELLED G-PRIMER, a web-based primer design program, has been developed to compute a minimal primer set specifically annealed to all the open reading frames in a given microbial genome. This program has been successfully used in the microarray experiment for analyzing the expression of genes in the Xanthomonas campestris genome. AVAILABILITY It is available at http://mammoth.bii.a-star.edu...

SUMMARY ExPrimer is a web-based computer program to design primers mainly from a specified exon-exon junction (E-E-jn) of a gene of interest. The tool suggests the optimum primer-pair(s) of which the right (reverse) primer represents a particular E-E-jn of the mRNA. The 'product length' decides the location of the left primer. The results also include all other primer pairs considered and their...

The analysis of DNA methylation at CpG dinucleotides has become a major research focus due to its regulatory role in numerous biological processes, but the requisite need for assays which amplify bisulfite-converted DNA represents a major bottleneck due to the unique design constraints imposed on bisulfite-PCR primers. Moreover, a review of the literature indicated no available software solutio...

Polymerase chain reaction-amplified product length polymorphism (PCR-APLP) is one of the most convenient and reliable methods for single nucleotide polymorphism (SNP) analysis. This method is based on PCR, but uses allele-specific primers containing SNP sites at the 3'-terminus of each primer. To use this method at least two allele-specific primers and one "counter-primer", which serves as a co...

BACKGROUND Polymerase chain reaction (PCR) is one of the most important developments in modern biotechnology. However, PCR is known to introduce biases, especially during multiplex reactions. Recent studies have implicated the DNA polymerase as the primary source of bias, particularly initiation of polymerization on the template strand. In our study, amplification from a synthetic library conta...

1 Biological scientists often need to design primers. These are short pieces of DNA used for copying sections of a DNA sequence using the polymerase chain reaction (PCR). Primers have various properties that influence the likelihood of success and scientists wish to quickly and easily select the best primers for amplification of a target sequence. Current web-based primer design software (Prime...

Objective. Low gene expression in rare cell subpopulations can make it difficult to identify transcripts using real time quantitative RT-PCR (qRT-PCR). Transcript number can be increased using linear amplification, but this technique amplifies the 3’ end of mRNA, imposing severe limitations on qRT-PCR primer design. Artifacts such as primer-dimers, introduced by these limitations, may interfere...

Decomposable models and Bayesian net­ works can be defined as sequences of oligo­ dimensional probability measures connected with opemtors of composition. The prelim­ inary results suggest that the probabilistic models allowing for effective computational procedures are represented by sequences pos­ sessing a special property; we shall call them perfect sequences. The present paper lays down th...