Frequently Asked Questions
| What are the goals of this project? |
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| The primary goal of the project is to discover and map single nucleotide polymorphisms in tetraploid and hexaploid wheat and develop appropriate bioinformatic tools for public access to this resource. The secondary goal is to employ this resource in preliminary characterization of genetics structure of the genepools of tetraploid and hexaploid wheat and wheat diploid ancestors. |
| What does the Wheat SNP Database contain? |
| This database includes conserved and genome-specific PCR primers (for amplification of STSs from genomic DNA of wheat and its diploid and tetraploid ancestors), DNA sequences, sequence annotations, intron/exon predictions, electropherograms, haplotypes, SNPs, and positions of SNP markers on wheat linkage maps. |
| How do I use "How To"? |
| On almost every page of this tool you will see a gray rectangle at the top left-hand corner of the screen with the label "How To". Simply click on the small downward arrow icon to open a menu of help topics. Click on the one you want and follow the directions. |
| What is a locus/loci? |
| A Polymorphism Locus is a section of one of our Contigs that has been sequenced to identify polymorphisms across lines. It is generally assigned to both a physically mapped Expressed Sequence Tag (EST) Accession Identifier and a Contig Name, except in cases where the EST is the Contig, in which cases it should be identified as a Singleton Contig and will only be identified by EST Accession Id. The Polymorphism Loci are one of the three core units of data on these pages, and can be reached through several different routes. The simplest is to search for the Locus directly using one or several fields. Simply click on the "search" link at the top left-hand corner of this page, and when the Search Page appears, open the "How To" help menu. It's also possible to access this data by looking at physical representations of the hexaploid wheat genomes, which we call ideograms, and which allow you to drill down on a specific region of a specific chromosome to view all the experimental data collected in that region. Simply click on the "ideograms" link at the top left-hand corner of this page, then open the "How To" help menu and follow the directions there. Finally, you can access this data indirectly, by searching for a given primer or sequence and then choosing various links, like 'EST Accession', which will drop you back into the polymorphism data. Since the polymorphism data is really the centerpiece of this tool, almost everywhere you go will eventually lead you back to it. |
| What is verified/unverified data? |
| There are two kinds of polymorphism loci in this database, those that have been experimentally confirmed to be genome-specific and those which are simply predicted to exist on a specific genome. Those that have been experimentally confirmed are listed as 'verified' and those that have not are listed as 'unverified'. |
| How do I find a sequence? |
| The amplicon sequences that were used to derive the polymorphism data here are also available to search or browse. The central "Search" page has a section dedicated to searching for sequences, and the "Sequences" page allows you to drill down to specific sequence data beginning with the lab that performed the investigation. |
| How do I find a primer? |
| Primer data is also available through this tool, and can be searched for on the central search page or selected for on several different pages. For example, once you've pulled up information for a specific polymorphism locus, you can click on the primer names and see detailed information on the primers used to amplify that region. |