PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

Bioinformatics. 2011 Apr 15;27(8):1159-61. doi: 10.1093/bioinformatics/btr087. Epub 2011 Feb 23.


Motivation: PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task.

Results: PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.

Availability: PrimerProspector is open-source software available at


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA Primers / chemistry*
  • Humans
  • Phylogeny
  • Polymerase Chain Reaction*
  • Sequence Alignment
  • Software*


  • DNA Primers