Please cite as: CSH Protocols; 2007; doi:10.1101/pdb.prot4786

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SNP Mining from Maize 454 EST Sequences

W. Brad Barbazuk1,4, Scott Emrich2, and Patrick S. Schnable3

1Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
2Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
3Department of Agronomy; Department of Genetics, Development, and Cell Biology; and Center for Plant Genomics; Iowa State University, Ames, IA 50011, USA

4Corresponding author (bbarbazuk{at}danforthcenter.org)


INTRODUCTION

In this protocol, 454 expressed sequence tags (ESTs) are generated by sequencing shoot apical meristem (SAM) cDNA from maize inbred lines on the 454 Life Sciences GS-20 sequencing system. The computational tool PolyBayes (Marth et al. 1999) is then used to identify single-nucleotide polymorphisms (SNPs). PolyBayes has been used successfully to identify SNPs in many different systems, including maize, and is particularly recommended for identifying SNPs in 454 sequences.


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