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Bioinformatics Advance Access published online on June 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth360
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 2, 2004
Revised May 29, 2004
Accepted May 31, 2004

Applications note

SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays

Tianhua Niu 1* Zhenjun Hu 2

1 Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, 900 Commonwealth Ave., MA 02215
2 Bioinformatics Program, Boston University, Boston, MA 02215

* To whom correspondence should be addressed. E-mail: tniu{at}hsph.harvard.edu.


  Abstract

Summary: Simple, low-cost, and accurate genotyping methods for single nucleotide polymorphisms (SNPs) are in high demand in the post-genome-sequencing era. We present a graphical tool called SNPicker, implemented in Java, which significantly facilitates the design of mutagenic endonuclease restriction assays. SNPicker uses the online NEB REBASE to automatically scan for all possible designs of mutagenic primers that can facilitate the picking of mismatched PCR primers to artificially introduce or abolish a restriction site at the target SNP site. We successfully applied SNPicker in designing endonuclease restriction assays for 14 SNPs for the MTHFR gene, the Coagulation Factor II gene, and the Coagulation Factor V gene. The SNP assays designed using SNPicker were cross-validated using the MassARRAY technology.

Availability: SNPicker, as a software tool in the Web-based SeqVISTA Suite, is freely available at http://zlab.bu.edu/SeqVISTA/. A tutorial for SNPicker is available at http://zlab.bu.edu/SeqVISTA/manual/SNPicker.htm.


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