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Bioinformatics Vol. 17 no. 9 2001
Pages 840-842
© 2001 Oxford University Press

Applications Note

Detecting the impact of sequencing errors on SAGE data

Jacques Colinge 1,2 and Georg Feger 1,*

1 Serono Pharmaceutical Research Institute, Ch. des Aulx 14, CH-1228 Plan-les-Ouates, Switzerland

Received on March 13, 2001 ; revised on May 30, 2001 ; accepted on June 7, 2001

Summary: SAGE data are obtained by sequencing short DNA tags. Due to the mistakes in DNA sequencing, SAGE data contain errors. We propose a new approach to identify tags whose abundance is biased by sequencing errors. This approach is based on a concept of neighbourhood: abundant tags can contaminate tags whose sequence is very close. The application of our approach reveals that moderately abundant tags can be generated by sequencing errors uniquely. It also allows for detecting correct rare tags.

Availability: Software is available only to non-profit entities and for non-commercial purposes upon request.

Contact: Georg.Feger{at}serono.com

* To whom all correspondence should be addressed.

2 Present address: GeneProt Inc., Pré-de-la-Fontaine 2, CH-1217 Meyrin, Switzerland.


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