Quick Queries

Expedited access to some of GrainGenes' most Frequently Asked Queries.
We'd like to have all the GrainGenes FAQs available right here.
You can help!
If you have a GrainGenes question you want to ask, please let me know. Somebody else probably has the same question.
- Dave, matthews@greengenes.cit.cornell.edu

References

• Choose by author, keyword and/or date. (Author and Keyword can be left blank. "since" must be a number.)
  Author     Keyword,    since

Microsatellites and STS's

SSR primers and corresponding mapped loci.
Improvements suggested by Christie Williams and Simon Berry.
BARC* Bmac* Bmag* CFA* CFD* EBma* GDM* Hv* SCM* WMC* WMS* * SSR set (* for all)
Primers
Map locations on chromosome (* for all)
Mapping data: segregation scores for these SSRs in all populations for which we have the data.
• STS primers
  "Sequence-Tagged Sites", primers designed to amplify specific sequences.

Markers and mapped genes

• Download a whole map (Map_Data)
  Linkage groups, Loci and positions, and the corresponding Probes.
  Suggested by Gramene.
  Map_Data name   List all Map_Data names
• Nearby Loci
  All Loci that are within a specified distance of a specified Locus on any map.
  Suggested by Jim Anderson; improved by Yavuz Barbaros.
  Locus
  Distance     List all Loci
  • Nearby Genes - A modification that shows only the Genes near the specified locus.
    Suggested by Angelo Karakousis and Victor Aguilar.
    Locus
    Distance     List all Loci

• Loci between two markers
  All Loci that are between two specified Loci on any map.
  Suggested by Molly Jahn and Gilly Sanchez.
  Locus 1
  Locus 2   List all Loci
• Trait markers - Linkages between useful genes and molecular markers.
  From Greg Penner's 2_Point_Data database.

• All maps for a given Probe  
  Suggested by Mark Sorrells.
• Genes by chromosome group - Genes mapped to a specified chromosome group. (Default is group 1.)
  Suggested by Angelo Karakousis.

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

Sequences

• Mapped sequences - Probes that are mapped and sequenced.
  • Loci for a specified sequence (GenBank Accession)
    Suggested by Tim Close.
  • Loci homologous to a specified sequence (GenBank Accession)
    
  • Probes homologous to a sequence of specified function (Keyword)
    GrainGenes Database (Use wildcard *s.) Mapping probes that are sequenced.
    New! wEST-SQL (Don't use wildcard *s.) Mapped ESTs from the NSF project.
    Suggested by Jose Gonzalez-Hernandez.

• ESTs homologous to sequences from a particular species
  Suggested by Shahryar Kianian.
• Sequenced genes - Listed by Gene Class. With map location if available.
  Suggested by Peter Mascia.

• Mapped known-function probes - Cloned genes that have been mapped in barley. (The barley restriction can be changed by editing the query.)
  Suggested by Peter Hedley; improved by Barbara Read.

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

• EST contigs vs. libraries - Compare treatments that produced ESTs in the same Contig.
  Treatment 1
  Treatment 2       List all Treatments
  Suggested by Tim Close.

Genes

• Barley genes - Symbols, synonyms, chromosomes and references for Hordeum genes. Most of these are from Knowles (1993), and Barley Genetics Newsletter volume 26; other major sources are the Wheat Gene Catalogue, and Joergensen (1993)'s catalogue of Ml genes.

Polymorphisms

• Allele differences (polymorphisms) between two germplasm lines
  
  

• Allele identities (monomorphisms) between two germplasm lines
  
  Suggested by Michael Wanous.

Germplasm

• 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.

Addressbook

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