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Bioinformatics Vol. 18 no. 8 2002
Pages 1137-1138
© 2002 Oxford University Press

Applications Note

ShiftDetector: detection of shift mutations

Eyal Seroussi 1,*, Micha Ron 1 and Darek Kedra 2

1 Institute of Animal Science, Volcani Center, Bet-Dagan 50250, Israel
2 Information Systems Department, The Burnham Institute, La Jolla CA 92037, USA

Received on October 21, 2001 ; revised on February 3, 2002 ; accepted on March 4, 2002

Motivation: Sequencing of a bi-allelic PCR product, which contains an allele with a deletion/insertion mutation results in a superimposed tracefile following the site of this shift mutation. A trace file of this type hampers the use of current computer programs for base calling. ShiftDetector analyses a sequencing trace file in order to discover if it is a superimposed sequence of two molecules that differ in a shift mutation of 1 to 25 bases. The program calculates a probability score for the existence of such a shift and reconstructs the sequence of the original molecule.

Availability: ShiftDetector is available from http://cowry.agri.huji.ac.il

Contact: seroussi{at}agri.huji.ac.il

* To whom correspondence should be addressed.


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