MOTIVATION DNA methylation plays important roles in biological processes and human diseases, especially cancers. High-throughput bisulfite genomic sequencing based on new generation of sequencers, such as the 454-sequencing system provides an efficient method for analyzing DNA methylation patterns. The successful implementation of this approach depends on the use of primer design software capab...

Polymorphism. A Hinf I PCR-RFLP was identified in the porcine leptin receptor ( LEPR) gene. Source and Description of Primers. Human cDNA (GenBank accession no. U43168) sequence was used to design primers to amplify porcine genomic DNA. Primer Sequences. Forward primer: 5¢GCATCCCATATCTGAACCC3¢; reverse primer: 5¢-CCACTTAAACCATAGCGAATC3¢.

Spurious Motifs.Our algorithm finds all positions in the strings that meet the specified requirements and will report no positions that do not; this is its advantage in contrast to algorithms in [5] and [3]. However, it clearly cannot exclude to find spurious motifs, e.g., random motifs in artificially generated data that have not been implanted. Note that not all combinations of L and d values...

A short-term electricity market coordinated by a system operator provides a foundation for a competitive electricity market. Combined with long-term contracts for generation and transmission congestion, the spot-market and competitive market pricing can support open access to the transmission grid. INTRODUCTION Electricity market restructuring emphasizes the potential for competition in generat...

BISTRO-PRIMER TOOL TO DESIGN AND VALIDATE SPECIFIC PCR PRIMER PAIRS FOR PHYLOGENETIC ANALYSIS Praful Aggarwal Marquette University, 2011 Polymerase Chain Reaction is a widely used biological technique which helps in amplifying small quantities of DNA. These amplified DNA copies are then used in several other experiments like DNA sequencing, phylogenetic analysis, etc. PCR primers are short subs...

The web application PCR Suite is an extension of the primer design program Primer3. It allows the design of primer sets encompassing single nucleotide polymorphisms, all exons of a single gene, all open reading frames in a list of cDNAs or the creation of overlapping PCR products.

We developed a primer design method, Pythia, in which state of the art DNA binding affinity computations are directly integrated into the primer design process. We use chemical reaction equilibrium analysis to integrate multiple binding energy calculations into a conservative measure of polymerase chain reaction (PCR) efficiency, and a precomputed index on genomic sequences to evaluate primer s...

UNLABELLED The design of genetic markers is of particular relevance in crop breeding programs. Despite many economically important crops being polyploid organisms, the current primer design tools are tailored for diploid species. Bread wheat, for instance, is a hexaploid comprising of three related genomes and the performance of genetic markers is diminished if the primers are not genome specif...

UNLABELLED Designed degenerate primers unlike conventional primers are superior in matching and amplification of large number of genes, from related gene families. DPPrimer tool was designed to predict primers for PCR amplification of homologous gene from related or diverse plant species. The key features of this tool include platform independence and user friendliness in primer design. Embedde...

TaqMan, a variation of fluorescent PCR, is a powerful tool for gene expression and polymorphism studies. Here we describe the design and evaluation of 27 new TaqMan primer-probe sets for rat genes that play a key role in neural signaling. These newly designed and synthesized probes were tested and then used for quantification of RNA isolated from rat brain. The usual length of common TaqMan pro...