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Bioinformatics Advance Access published online on December 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/btk006
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 29, 2005
Revised November 23, 2005
Accepted December 11, 2005

Applications note

SEAN: SNP prediction and display program utilizing EST sequence clusters

Derek Huntley 1 *, Angela Baldo 2, Saurabh Johri 3, and Marek Sergot 4

1 Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College, London SW7 2AZ UK
2 USDA-ARS Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Geneva, NY 14456-0462, USA
3 Centre for Molecular Microbiology and Infection, Division of Investigative Sciences, Imperial College, London SW7 2AZ UK
4 Department of Computing, Imperial College, London SW7 2AZ

* To whom correspondence should be addressed.
Derek Huntley, E-mail: d.huntley{at}imperial.ac.uk


  Abstract

Summary: SEAN is an application that predicts SNPs using multiple sequence alignments produced from EST clusters. The algorithm uses rules of sequence identity and SNP abundance to determine the quality of the prediction. A Java viewer is provided to display the EST alignments and predicted SNPs.

Availability: SEAN is freely available from http://zebrafish.doc.ic.ac.uk/Sean.


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