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Bioinformatics Vol. 19 no. 3 2003
Pages 421-422
© 2003 Oxford University Press

Applications Note

Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP

Gary Barker 1, Jacqueline Batley 2, Helen O’ Sullivan 1, Keith J. Edwards 3 and David Edwards 2,*

1 Institute of Arable Crop Research, Long Ashton, Bristol, BS41 9AF, UK
2 Agriculture Victoria Plant Biotechnology Centre, La Trobe University, Bundoora, Victoria 3086, Australia
School of Biological Sciences, University of Bristol BS8 1UG, UK

Received on June 28, 2002 ; revised on August 23, 2002 ; accepted on August 28, 2002

Summary: AutoSNP is a program to detect single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels) in expressed sequence tag (EST) data. The program uses d2cluster and cap3 to cluster and align EST sequences, and uses redundancy to differentiate between candidate SNPs and sequence errors. Candidate polymorphisms are identified as occurring in multiple reads within an alignment. For each candidate SNP, two measures of confidence are calculated, the redundancy of the polymorphism at a SNP locus and the co segregation of the candidate SNP with other SNPs in the alignment.

Availability: The program was written in PERL and is freely available to non-commercial users by request from the authors.

Contact: dave.edwards{at}nre.vic.gov.au

* To whom correspondence should be addressed.


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