Download Welcome to the Gene and Allele Database Tutorial

Gramene v. 26
Welcome to the Gene
and Allele Database Tutorial
This tutorial will describe how to navigate the
section of Gramene that provides
descriptions of alleles associated with
morphological, developmental, and
agronomically important phenotypes and
variants of physiological characters,
biochemical functions and isozymes.
Many genes in Gramene also have map
positions and sequencing data.
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Tutorial Tips
If you are viewing this tutorial with Adobe
Acrobat Reader, click the "bookmarks"
on the left hand side of the Reader for
easier navigation.
Note! Although we continually work to make Gramene compatible with
all browsers, there are problems with some browser versions. If you're
having difficulty viewing Gramene, try using a different browser. Please
report any problems with browsers through Gramene Feedback.
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www.gramene.org
Gramene Home Page
Click here to open gene
search
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See Navigation Tutorial for info on
navigating Gramene
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Module Home-Page layout
Module home pages provide the following information:
• Searching/Browsing – links to different types of searches.
• Other Tools – if applicable, links to different tools used in this module.
• Help – links to help pages, tutorials, release notes, FAQ and other helpful
documentation.
• Download – information on where to download the database.
• Feedback – How to contact Gramene
• Acknowledgements – Other programs that contribute to this data.
• Quicklinks and external links – when appropriate these links are
provided.
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Gene & Allele Database Home Page
Use * to search for
wildcards
1. Use the
“search” link
from the gene
menu to select a
more limited
(specific) search.
(see slide 5) or
2. Use the general
search option.
Explains module
navigation menu,
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Search Options
Option 1. Click an ontology to
search ontologies db.
Option 2. Search
by term
Click search
icon
Be aware of wildcards.
For example, searches for
*dwarf, dwarf*, and
*dwarf* will all give
different results.
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Optionally, select field name, gene type,
species, and whether or not the gene
is associated with a known
phenotype.
Option 3. You may also browse for a gene via Literature
Database. Go to the Literature Database in Gramene.
Literature detail will display genes in the “Associated Data"
field.
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Results for Gene Search by Term / Key word
There are 99 entries for rice genes
with CDS and phenotype
Click on a gene symbol to view the detail
page for that particular gene (for tutorial
select “d1” and see slide 9)
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Click to view next 25 results
as needed.
Click on linked
column headings to
sort table by that
column
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Gene Detail Page General Info
Gene detail is displayed along the top.
See Help file for term definitions.
Associated Data is under the Gene detail. The number
represent numbers of associations. Click a category to
expand the table and access that data in Gramene (see
slides 8–13). Grayed-out categories have no associations.
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Gene detail may vary by species, depending
upon level of curation.
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Gene Associations – Allele and Germplasm Info
Links to Ontology DB
Allele and Germplasm
categories show one or
multiple items for a
particular gene. Click a
name to view its summary
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Gene Associations - Sequences
Click on protein to view more
information from Gramene’s
Protein database (See Protein
tutorial). Link to GenBank for
sequence info
Click GenBank ID to view
the nucleotide sequence link
for each protein from the
National Center for
Biotechnology Information.
Select Ensemble Gene to view Tigr
gene report in Genomes database
(See Genomes tutorial).
Click on IRGSP gene name to go to the
Rice Annotation Project DB (RAP-DB)
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Gene interactions
If it is known that a gene
interacts with another gene, that
will be noted here.
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Genes – Map Positions
Preview comparative map
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Select to view the highlighted gene in Maps or on the
genome browser (See Maps and Genomes tutorials).
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Genes – associated ontologies
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Click links to go to the Ontology
Database within Gramene. (See
Ontology tutorial).
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Gene - Associated References
Click to view Oryzabase’s information
on the selected gene.
Click reference info to go to the reference
in Gramene Literature database (See
Literature tutorial).
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Gene - Images
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When there are images in the database
associated with a phenotype gene, they will
display here.
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How to Submit Newly Identified Genes
Click here to submit a
gene to the database.
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Help Documents
Help documentation gives detailed notes
about the information found in the
database, and help on using the search
tools.
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Tutorial
Tutorial shows the features of a database.
Tutorials come in PowerPoint and PDF.
Some are also available in MS Word.
Navigate to other
Gramene tutorials.
Links to download software for
viewing tutorials.
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FAQ’s
Feedback: Submit a
question to Gramene
Search FAQ
Click questions to expand or
collapse a question or answer
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Contact Gramene
Use the feedback button, located at the top of every page, to
provide feedback or to ask questions about Gramene.
or
Email Gramene List-serve at [email protected]
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