Design primers to amplify any locus in human, mouse and rat genomes.

Utilizing polymerase chain reaction (PCR) to amplify genomic regions has become a routine approach to detect abundancy or sequence variations, such as preferentially enrichment of protein binding segments in Chromatin Immunoprecipitation (ChIP) assay or genotyping single nucleotide polymorphisms (SNP). These experimentations usually demand high throughput PCR methods for optimal amplification of multiple targets based solely on genomic landmark, coordinate or genic component. We developed an online service, PrimerWise, which designs real time PCR primers to amplify a segment flanking a user defined nucleotide. This nucleotide can be a genomic coordinate, or any distance from a genic component, such as exon or intron. All primers have unified annealing temperatures of approximately 60C which allows high throughput implementation of multiple primer sets. Primers are free of SNPs or repeatitive element and validated by in silico PCR. Candidate primer sets and their corresponding amplicons are illustrated in UCSC Genome Browser and NCBI Map Viewer.

Currently, this tool has full coverage of the following genomes:

Common Name	Species	Build	UCSC Version
Human	Homo sapiens	NCBI Build 36	hg18
Mouse	Mus musculus	NCBI Build 37	mm9
Rat	Rattus norvegicus	HGSC 3.4	rn4
Chicken	Gallus gallus	WASHUC2	galGal3

1. Choose an organism:

Organism:

2. Design primers using one the following options:

	For a gene. Please input a standard gene name like 'JUN':

	For a Refseq cDNA. Please input a Refseq ID like 'NM_001234':

	For a genomic location. Please select a chromosome number and input a coordinate:
	Chromosome: , Position:

Email: webmaster@genenformics.com