Quick Queries

The GrainGenes Database can generate reports containing the values of desired fields as columns of a table, where each column can be the result of a query.

Below are a few pre-defined reports I've made that may be generally useful. You can modify any of these, or create a new one, by clicking the "Modify table definition" button.

If you create a report you think might be useful to others, please save it ("save table definition") and let me know so I can add it to this menu. Or if you have a question but don't know how to ask it, let me know that too. I'm pretty good with these, plus I can modify the database to make things queryable that ought to be already but aren't.

- Dave, matthews@greengenes.cit.cornell.edu

• Allele differences (polymorphisms) between two germplasm lines
  
  
  Allele identities (monomorphisms) between two germplasm lines
  
  Suggested by Michael Wanous.
• Genes by chromosome group - Genes and their mapped locations for a specified chromosome group. (Default is group 1.)
  Suggested by Angelo Karakousis.

• Trait markers - Linkages between useful genes and molecular markers. From Greg Penner's 2_Point_Data database.

• Nearby Loci - All Loci that are within 10 cM of a specified Locus on any map. Enter the desired locus in the definition of Column 1. (Default is *cdo64*.)
  To use a search range other than 10 cM, click here for instructions.
  Suggested by Jim Anderson.
  • Nearby Genes - A modification that shows only the Genes near the specified locus. Default range 20 cM.
    Suggested by Angelo Karakousis.

• Probes mapped to a specified chromosome - (Default is 1D.)
  Suggested by Jon Raupp.

• PCR primers - Probes for which GrainGenes has information on specific primers (RAPDs excluded).

• Microsatellites - SSR primers and corresponding mapped loci.
  Improvements suggested by Christie Williams.

• Sequenced genes - Listed by Gene_Class. With map location if available.
  Suggested by Peter Mascia.

• Mapped sequences - (also known as Sequenced loci). Probes that have both Locus and Sequence data.

  • Map positions for a specified sequence (GenBank Accession)
    Suggested by Tim Close.
• Mapped and BLASTed sequences - Probes that have both Locus and Sequence BLAST homology data.

• Mapped known-function probes - Cloned genes that have been mapped in barley. (The barley restriction can be removed or altered by editing the condition "Species = Hordeum*" in the first column definition.) To get the complete results you need to combine two different sets:
  • Part 1 - Loci that have Candidate_genes.
  • Part 2 - Loci whose Probes have Source_gene_classes.
  Suggested by Peter Hedley.

• Mapped STS's - the FASTA sequence data only.
  Suggested by Philippe Leroy.

• Barley genes - Symbols, synonyms, chromosomes and references for Hordeum genes. Most of these are from Knowles (1993), and Franckowiak and Lundqvist (unpublished); other major sources are the Wheat Gene Catalogue, and Joergensen (1993)'s catalogue of Ml genes.

• Resistant germplasm - Accessions rated as "Resistant" or "Immune" or "Low sporulation" from the Wheat Genetics Resource Center. (Note: not all of the WGRC collection is in the database yet.)
  Suggested by Jon Raupp.

• ICARDA durums - Names, ICARDA accession numbers and pedigrees.

• Colleagues - All colleagues for which GrainGenes contains an electronic mail address or a photograph, or both.