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Open Access Software

CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping

Jonathan Taylor1 and Nicholas J Provart2*

Author Affiliations

1 Department of Computer Science, University of Toronto, 40 St George Street, Toronto, ON M5S 2E4, Canada

2 Centre for the Analysis of Genome Evolution and Function, Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada

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BMC Genetics 2006, 7:27  doi:10.1186/1471-2156-7-27

Published: 10 May 2006



Genotyping may be carried out by a number of different methods including direct sequencing and polymorphism analysis. For a number of reasons, PCR-based polymorphism analysis may be desirable, owing to the fact that only small amounts of genetic material are required, and that the costs are low. One popular and cheap method for detecting polymorphisms is by using cleaved amplified polymorphic sequence, or CAPS, molecular markers. These are also known as PCR-RFLP markers.


We have developed a program, called CapsID, that identifies snip-SNPs (single nucleotide polymorphisms that alter restriction endonuclease cut sites) within a set or sets of reference sequences, designs PCR primers around these, and then suggests the most parsimonious combination of markers for genotyping any individual who is not a member of the reference set. The output page includes biologist-friendly features, such as images of virtual gels to assist in genotyping efforts. CapsID is freely available at webcite.


CapsID is a tool that can rapidly provide minimal sets of CAPS markers for molecular identification purposes for any biologist working in genetics, community genetics, plant and animal breeding, forensics and other fields.