Web-based primer design for single nucleotide polymorphism analysis

Trends Genet. 2002 Dec;18(12):613-5. doi: 10.1016/s0168-9525(02)02820-2.


The detection of single nucleotide polymorphisms by PCR is necessary for many types of genetic analysis, from mapping genomes to tracking specific mutations. This technique is most commonly used when polymorphisms alter restriction endonuclease recognition sites. Here we describe a web-based program, dCAPS Finder 2.0, that facilitates the design of mismatched PCR primers to create or remove a restriction endonuclease recognition site relative to the polymorphism being analyzed.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis Proteins
  • Computer-Aided Design*
  • Cryptochromes
  • DNA Primers*
  • Drosophila Proteins*
  • Eye Proteins*
  • Flavoproteins / genetics
  • Genetic Markers
  • Haplotypes
  • Photoreceptor Cells, Invertebrate*
  • Polymorphism, Restriction Fragment Length
  • Polymorphism, Single Nucleotide*
  • Receptors, G-Protein-Coupled
  • Sequence Analysis, DNA / methods


  • Arabidopsis Proteins
  • CRY1 protein, Arabidopsis
  • Cryptochromes
  • DNA Primers
  • Drosophila Proteins
  • Eye Proteins
  • Flavoproteins
  • Genetic Markers
  • Receptors, G-Protein-Coupled
  • cry protein, Drosophila