Cite as: Cold Spring Harb. Protoc.; 2007; doi:10.1101/pdb.prot4786

This Protocol
Right arrow Full Text
Right arrow Update/discuss this protocolDiscussion icon
Right arrow Alert me when this protocol is cited
Right arrow Alert me when comments are published
Right arrow Alert me if a correction is posted
Services
Right arrow Similar protocols in this database
Right arrow Alert me to new releases of protocols
Right arrow Save to Personal Folders
Right arrow Download to citation manager
Right arrow Printer-friendly versionPrinter-friendly version
Citing Articles
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Barbazuk, W. B.
Right arrow Articles by Schnable, P. S.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Barbazuk, W. B.
Right arrow Articles by Schnable, P. S.
Related Collections
Right arrow Plant Cell Culture
Right arrow Bioinformatics/Genomics, general
Right arrow Alignment of Sequences
Right arrow Alignment of Sequences, general
Right arrow Multiple Sequence Alignment
Right arrow Sequence Database Searching
Right arrow Computational Biology
Right arrow Genetics, general
Right arrow Genetic Variation
Right arrow Laboratory Organisms, general
Right arrow Molecular Biology, general
Right arrow Analysis of Gene Expression
Right arrow Analysis of Gene Expression, general
Right arrow cDNA
Right arrow DNA Sequencing
Right arrow RNA
Right arrow RNA, general
Right arrow mRNA
Right arrow Genome Analysis
Right arrow Expression Analysis of RNA
Right arrow Genomic Analysis
Right arrow Plant
Right arrow Analysis of Gene Expression in Plants
Right arrow Expression Libraries
Right arrowRelated Protocols
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati   Add to Twitter  
What's this?
BSN globe

protocolProtocol

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati   Add to Twitter Twitter    What's this?

Related Protocols

Maize Tissue Preparation and Extraction of RNA from Target Cells for Genotyping
Kazuhiro Ohtsu and Patrick S. Schnable
CSH Protocols 2007: 4784. [Abstract] [Full Text]

T7-Based RNA Amplification for Genotyping from Maize Shoot Apical Meristem
Kazuhiro Ohtsu and Patrick S. Schnable
CSH Protocols 2007: 4785. [Abstract] [Full Text]