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Welcome to the Gene and Allele Database Tutorial

Gramene v. 26. Welcome to the Gene and Allele Database Tutorial.

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Welcome to the Gene and Allele Database Tutorial

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  1. 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.

  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.

  3. Gramene Home Page www.gramene.org Click here to open gene search See NavigationTutorialfor info on navigating Gramene

  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.

  5. 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,

  6. Search Options Option 1. Click an ontology to search ontologies db. Option 2. Search by term 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 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.

  7. Results for Gene Search by Term / Key word There are 99 entries for rice genes with CDS and phenotype Click to view next 25 results as needed. Click on linked column headings to sort table by that column Click on a gene symbol to view the detail page for that particular gene (for tutorial select “d1” and see slide 9)

  8. 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. Gene detail may vary by species, depending upon level of curation.

  9. 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

  10. 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)

  11. Gene interactions If it is known that a gene interacts with another gene, that will be noted here.

  12. Genes – Map Positions Preview comparative map Select to view the highlighted gene in Maps or on the genome browser (See Maps and Genomes tutorials).

  13. Genes – associated ontologies Click links to go to the Ontology Database within Gramene. (See Ontology tutorial).

  14. 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).

  15. Gene - Images When there are images in the database associated with a phenotype gene, they will display here.

  16. How to Submit Newly Identified Genes Click here to submit a gene to the database.

  17. Help Documents Help documentation gives detailed notes about the information found in the database, and help on using the search tools.

  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.

  19. FAQ’s Feedback: Submit a question to Gramene Search FAQ Click questions to expand or collapse a question or answer

  20. 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 gramene@gramene.org

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