title: PrimerView: high-throughput primer design and visualization.
abstract: BACKGROUND
  High-throughput primer design is routinely performed in a wide number of molecular applications including genotyping specimens using traditional PCR techniques as well as assembly PCR, nested PCR, and primer walking experiments. Batch primer design is also required in validation experiments from RNA-seq transcriptome sequencing projects, as well as in generating probes for microarray experiments. The growing popularity of next generation sequencing and microarray technology has created a greater need for more primer design tools to validate large numbers of candidate genes and markers.
  
  
  RESULTS
  To meet these demands I here present a tool called PrimerView that designs forward and reverse primers from multi-sequence datasets, and generates graphical outputs that map the position and distribution of primers to the target sequence. This module operates from the command-line and can collect user-defined input for the design phase of each primer.
  
  
  CONCLUSIONS
  PrimerView is a straightforward to use module that implements a primer design algorithm to return forward and reverse primers from any number of FASTA formatted sequences to generate text based output of the features for each primer, and also graphical outputs that map the designed primers to the target sequence. PrimerView is freely available without restrictions.
authors.affiliation: Department of Biological Sciences, The George Washington University, Science & Engineering Hall 5685, 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.forename: Damien M
authors.initials: DM
authors.lastname: O'Halloran
keywords: Genotyping; NGS; PCR; Perl; Primer design; Sequencing