Upload
boyd
View
38
Download
0
Tags:
Embed Size (px)
DESCRIPTION
Gramene v. 26. Welcome to the Gene and Allele Database Tutorial. - PowerPoint PPT Presentation
Citation preview
04/22/23 1
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.
Welcome to the Gene and Allele Database Tutorial
Gramene v. 26
04/22/23 2
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.
04/22/23 3
Gramene Home Page
Click here to open gene search
See Navigation Tutorial for info on navigating Gramene
www.gramene.org
04/22/23 4
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.
04/22/23 5
Gene & Allele Database Home Page
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.
Use * to search for wildcards
Explains module navigation menu,
04/22/23 6
Option 1. Click an ontology to search ontologies db.
Search Options
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.
Click search icon
Optionally, select field name, gene type, species, and whether or not the gene is associated with a known phenotype.Be aware of wildcards.
For example, searches for *dwarf, dwarf*, and *dwarf* will all give different results.
Option 2. Search by term
04/22/23 7
Results for Gene Search by Term / Key word
Click to view next 25 results as needed.
There are 99 entries for rice genes with CDS and phenotype
Click on linked column headings to
sort table by that columnClick on a gene symbol to view the
detail page for that particular gene (for tutorial select “d1” and see slide 9)
04/22/23 8
Gene detail is displayed along the top. See Help file for term definitions.
Gene Detail Page General Info
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.
Gene detail may vary by species, depending upon level of curation.
04/22/23 9
Allele and Germplasm categories show one or multiple items for a particular gene. Click a name to view its summary
Gene Associations – Allele and Germplasm Info
Links to Ontology DB
04/22/23 10
Gene Associations - SequencesClick 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)
04/22/23 11
Gene interactions
If it is known that a gene interacts with another gene,
that will be noted here.
04/22/23 12Select to view the highlighted gene in Maps or on the genome browser (See Maps and Genomes tutorials).
Genes – Map Positions
Preview comparative map
04/22/23 13
Click links to go to the Ontology Database within Gramene. (See Ontology tutorial).
Genes – associated ontologies
04/22/23 14
Click reference info to go to the reference in Gramene Literature database (See Literature tutorial).
Click to view Oryzabase’s information on the selected gene.
Gene - Associated References
04/22/23 15
Gene - Images
When there are images in the database associated with a phenotype gene, they
will display here.
04/22/23 16
How to Submit Newly Identified Genes
Click here to submit a gene to the database.
04/22/23 17
Help Documents
Help documentation gives detailed notes about the information found in the database, and help on using the search tools.
04/22/23 18
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.
04/22/23 19
FAQ’s
Search FAQ
Feedback: Submit a question to Gramene
Click questions to expand or collapse a question or answer
04/22/23 20
Contact Gramene
Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene.
Email Gramene List-serve at [email protected]
or