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PrimerView: high-throughput primer design and visualization.

Damien M O'Halloran1

  • 1Department 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.

Source Code for Biology and Medicine
|June 9, 2015
PubMed
Summary
This summary is machine-generated.

PrimerView is a new command-line tool for designing primers from multiple sequences. It provides graphical outputs to visualize primer placement, aiding in molecular biology applications.

Keywords:
GenotypingNGSPCRPerlPrimer designSequencing

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • High-throughput primer design is crucial for molecular applications like PCR and transcriptome validation.
  • Next-generation sequencing and microarrays increase the demand for efficient primer design tools.

Purpose of the Study:

  • To introduce PrimerView, a novel tool for designing primers from multi-sequence datasets.
  • To provide graphical outputs for visualizing primer position and distribution.

Main Methods:

  • PrimerView operates from the command-line.
  • It accepts user-defined input for primer design parameters.
  • The tool processes FASTA formatted sequences.

Main Results:

  • PrimerView designs forward and reverse primers from multi-sequence datasets.
  • It generates text-based output detailing primer features.
  • Graphical outputs map designed primers to target sequences.

Conclusions:

  • PrimerView is a user-friendly module for primer design.
  • It supports validation of numerous candidate genes and markers.
  • The software is freely available without restrictions.