PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR

Bioinformatics. 2004 Oct 12;20(15):2471-2. doi: 10.1093/bioinformatics/bth254. Epub 2004 Apr 8.


PerlPrimer is a cross-platform graphical user interface application for the design of primers for standard, bisulphite and real-time PCR, and sequencing. The program incorporates highly accurate melting-temperature and primer-dimer prediction algorithms with powerful tools such as sequence retrieval from Ensembl and the ability to BLAST search primer pairs. It aims to automate and simplify the process of primer design.

Availability: Open-source and freely available from

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Chromosome Mapping / methods*
  • DNA Primers / chemical synthesis
  • DNA Primers / genetics*
  • Oligonucleotide Array Sequence Analysis / methods
  • Online Systems
  • Polymerase Chain Reaction / methods*
  • Sequence Alignment / methods
  • Sequence Analysis, DNA / methods*
  • Software*
  • Sulfites
  • User-Computer Interface*


  • DNA Primers
  • Sulfites