SNP2CAPS - A SNP and INDEL analysis tool for CAPS marker development

The use of single nucleotide polymorphisms (SNPs) in genomes for marker assays has the potential to provide answers to a large number of important biological questions. Most of these assays require expensive and specialised equipment for analysis. However, cleaved amplified polymorphic sequences (CAPS) have shown to be robust and cost effective assays that can be implemented in laboratories that do not have access to sophisticated equipment. The principle of CAPS assays involves the PCR amplification of a SNP site and the detection of this site by an appropriate restriction endonuclease whose recognition sequence has been altered or introduced by the SNP. If done manually, the selection of suitable restriction endonuclease enzymes can be a difficult and time consuming process.

SNP2CAPS facilitates the computational conversion of SNPs into CAPS markers. A simple algorithm involves the screening of multiply-aligned sequences for restriction sites followed by a selection pipeline that allows the deduction of CAPS candidates by the identification of putative alternative restriction sites.

Download SNP2CAPS (Perl script)

Download SNP2CAPS (GUI Windows executable, 1.5 MB)

Required input files:

  1. Multiple alignment file:
  2. REBASE: restriction enzyme database (GCG-format data file, downloadable from


  1. GUI version of SNP2CAPS
  2. Requires an installed Perl distribution including the Tk module

    Invocation: -gui

  3. Command line version of SNP2CAPS
  4. Invocation: <msa_file> <rebase_db> <enzymes> > <output>

    <msa_file> file containing the multiple alignments
    <rebase_db> file containing the REBASE database in GCG format
    <enzymes> comma separated list of enzymes (e.g. EcoRV,BamHI)
    <output> save the results in the output file (optional)


Questions and comments: Thomas Thiel

Last updated: 11/10/03