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Open Access Research article

Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

Mauricio La Rota1, Ramesh V Kantety2, Ju-Kyung Yu1 and Mark E Sorrells1*

Author Affiliations

1 Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY, 14853, USA

2 Department of Plant & Soil Science, 138 ARC Building, Alabama A&M University, Normal, AL, 35762, USA

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BMC Genomics 2005, 6:23  doi:10.1186/1471-2164-6-23

Published: 18 February 2005

Additional files

Additional File 1:

EST-SSR designed primers Table listing the stringent subset of SSRs (≥ 16 bp tetranucleotides, ≥ 18 bp dinucleotides and trinucleotides, and ≥ 20 bp pentanucleotides) found in rice, barley and wheat gene indices for which primer sequences were designed, the source sequences, the primers, their in-silico mapping in the rice genome (to BAC/PAC clones or pseudo-molecule) and relevant metadata. File is a spreadsheet table, compressed with the zip program. The file (14 Mb uncompressed) is also available at the GrainGenes Triticeae EST-SSR Coordination page http://wheat.pw.usda.gov/ITMI/EST-SSR/LaRota/ webcite

Format: ZIP Size: 4MB Download file

Open Data

Additional File 2:

Modified Sputnik source code and executable This is the source code with modifications, to the microsatellite searching program "Sputnik", originally written by Chris Abajian from the University of Washington at Seattle. The set of files are compressed using the zip program. File is also available at http://wheat.pw.usda.gov/ITMI/EST-SSR/LaRota/ webcite

Format: ZIP Size: 358KB Download file

Open Data

Additional File 3:

Perl script to design primers in batch The script uses the Bioperl perl modules to control the Primer3 program in order to design primers from a microsatellite database stored in a MySQL database. The script can be modified to accommodate similar schemas on any database engine supported by the perl DBI module. File is also available at http://wheat.pw.usda.gov/ITMI/EST-SSR/LaRota/ webcite

Format: TXT Size: 12KB Download file

Open Data