title: PrimerMapper: high throughput primer design and graphical assembly for PCR and SNP detection.
abstract: Primer design represents a widely employed gambit in diverse molecular applications including PCR, sequencing, and probe hybridization. Variations of PCR, including primer walking, allele-specific PCR, and nested PCR provide specialized validation and detection protocols for molecular analyses that often require screening large numbers of DNA fragments. In these cases, automated sequence retrieval and processing become important features, and furthermore, a graphic that provides the user with a visual guide to the distribution of designed primers across targets is most helpful in quickly ascertaining primer coverage. To this end, I describe here, PrimerMapper, which provides a comprehensive graphical user interface that designs robust primers from any number of inputted sequences while providing the user with both, graphical maps of primer distribution for each inputted sequence, and also a global assembled map of all inputted sequences with designed primers. PrimerMapper also enables the visualization of graphical maps within a browser and allows the user to draw new primers directly onto the webpage. Other features of PrimerMapper include allele-specific design features for SNP genotyping, a remote BLAST window to NCBI databases, and remote sequence retrieval from GenBank and dbSNP. PrimerMapper is hosted at GitHub and freely available without restriction.
authors: Department of Biological Sciences, The George Washington University, Science and Engineering Hall 6000, 800 22nd St. N.W. Washington DC 20052, USA.|Institute for Neuroscience, The George Washington University, 636 Ross Hall, 2300 I St. N.W. Washington DC 20052, USA.
authors: Damien M
authors: DM
authors: O'Halloran
mesh_terms: D000483:Alleles; D017931:DNA Primers / Q000235:genetics / Q000378:metabolism*; D030541:Databases, Genetic; D005838:Genotype; D020407:Internet; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D014584:User-Computer Interface
chemical_list: D017931:DNA Primers