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Bioinformatics Vol. 18 no. 12 2002
Pages 1688-1689
© 2002 Oxford University Press

Applications Note

PCR designer for restriction analysis of various types of sequence mutation

Xiayi Ke 1,*, Andrew Collins 2 and Shu Ye 2

1 Wellcome Trust Centre For Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
2 Division of Human Genetics, University of Southampton, Duthie Building, Southampton General Hospital, Southampton SO16 6YD, UK

Received on March 20, 2002 ; revised on May 14, 2002 ; accepted on May 24, 2002

Summary: Restriction analysis is widely used to detect gene mutations such as insertions, deletions and single nucleotide polymorphisms (SNPs). Although such mutation sites sometimes present some natural restriction sites to differentiate the wild-type and mutant sequences, mismatches are often needed in order to create artificial restriction fragment length polymorphisms (RFLPs). In this report, a computer program is described that screens for suitable restriction enzymes, introducing mismatches where appropriate and when necessary, designs primers using the information of the selected restriction enzymes, their recognition sequence and locations as well as the information about the mismatches if any. The program, supported by a WWW web interface, is intended to be used online.

Availability: The computer software, with related documentation, is available at http://cedar.genetics.soton.ac.uk/public_html/primer.html

Contact: xiayi{at}well.ox.ac.uk

* To whom correspondence should be addressed.


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