Upload
scott-tracy-patterson
View
223
Download
0
Tags:
Embed Size (px)
Citation preview
Gramene V. 21 1
Gramene DiversityGramene Genetic Diversity database contains SSR and SNP allelic data and passport descriptions for rice, maize and wheat germplasms. It also holds
phenotypic data for maize.
The ultimate goal is to make this database a source of rice, maize, and wheat bio-information from/for
evolutionary, domestication, association, and genetic diversity studies. It also could potentially be useful for applications such as germplasm management, marker
assisted selection and DNA-based variety identification.
Gramene V. 21
2
Search by Germplasm
Passport DataAccession data
SynonymsHolding Institute
Stock SourceGermplasm
Taxonomy dtaCollection Data
Collector, LocationExperiment Data
TitleDesign
Polymorphism typeScoring Protocol
ProducerOriginatorCommentsAllele data
Marker and Allele DataAccession #
Accession nameLocus name
GenotypeAll genotypes on a marker/
germplasms
Search by Marker
Literature DB Markers DB
External germplasm DBs
Diversity Data Map
Gramene V. 21
3
Tutorial HelpThe hand icon indicates a link that allows you to go to the same page
in your web browser.
If you are viewing this tutorial with Adobe Acrobat Reader, click the "bookmarks" on the left hand side of the Reader for easier navigation.
Action Options are noted in this type of font.
Notes or comments use this style font.
Gramene V. 21
4
From either of the search or quick start menus, click on Diversity.
Gramene Home www.gramene.org
Gramene V. 21
5
1. Enter germplasm name, accession number or marker name to view allelic data. 2. Select species
Diversity Home: Search (by Germplasm name)
Example searches
Click for database species summaries (see Slide 13)
3. Click “Submit”
optional
General search does NOT search Diversity
Gramene V. 21
6
Error messages?
For accession numbers with IRGC
prefix, use quotations : “IRGC
3575“.
For small names (<3 letters/word) with a space, remove the
space : IR36
For small names (<3 letters) double the
name : T1T1
Error message gives hint
Gramene V. 21
7
Link(s) to external
databases
Link(s) to germplasm
request form(s)
Links to abstract
Click to view allele data on germplasm(see
Slide 8)
Click to view marker type details
Click to view taxonomic details (See Gramene Ontology
tutorial)
Search Results (Germplasm Name)
Passport Description
Collection Information
Experiment Information
Click to begin new search (home page)
Gramene V. 21
8
Allele Data (by Germplasm Accession #)
Return to Germplasm Data (Previous Slide)
Click for all allele data on this marker
(see Slide11)
Click for Marker Information
(Slide 9 & 10)
Markers assayed for a germplasm Allele(s) for the
corresponding loci
Gramene V. 21
9
See Slide 7 for more information on
details of this page.
Click to view marker details in Gramene
Marker DB. (See Slide 10)
Click to view allele data for marker from
experiment.(Slide 11)
Marker
Gramene V. 21
10
Marker Detail
Marker Data in Gramene Marker
DB. See Markers Tutorial
Markers menu indicates you are not in Diversity
database anymore
Gramene V. 21
11
Germplasm Data – as in slide 7.
All alleles for marker on all germplasms in an
experiment
Click to view all allele
data on all markers/loci
on a germplasm.
Allele Data for Marker
Gramene V. 21
12
Enter Marker name.
Click for database summary by species (see Slide 13)
Search result is the same as slides 9-11.
Search by Marker
Gramene V. 21
13
Data Summary
Summary of information in this
release of Gramene.
Gramene V. 21
14
Germplasm searchOptions are
based on species
Select options and click submit
Gramene V. 21
15
Molecular Diverisity Search
Options are based on species
Select options and click submit
Gramene V. 21
16
Gene/Locus Search
Options are based on species
Select options and click submit
Gramene V. 21
17
Phenotype Search
Options are based on species
Select options and click submit
Gramene V. 21
18
GDPC Browser
For more complex queries, you can use The Genomic Diversity and Phenotype Connection (GDPC) Browser. Here you can download and get documentation how to use the GDPC Browser.
Gramene V. 21
19
Use Feedback to ask questions or make
comments to Gramene
Help
Help documents assist in how to conduct a search and to define
your results.
Gramene V. 21
20
Tutorials
Tutorials are available in PDF or Powerpoint
All Gramene Tutorials listed here.
Click for other help documents
Gramene V. 21
21
FAQ’s
Select a module to view it’s FAQs
Search FAQ
Submit a question to Gramene
Gramene V. 21
22
Contact Gramene
Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene.
Email Gramene at [email protected]
or