1. Tutorial for: Gramene Website Navigation
Gramene v. 26
Tutorial for:
Gramene Website Navigation
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2. Accessing Gramene
To access Gramene, open your internet browser (such as Netscape, IE, or Safari).
(If some website features don’t work correctly, try using a different browser. We recommend a Mozilla based browser.)
This tutorial is a general introduction to Gramene website layout and navigation. Gramene developers work continuously to make the website compatible with all browsers, but if you have difficulty with website performance we recommend trying another browser.
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3. Option 1 -
In the address bar type “ and press “Enter” to open the Gramene Home Page.
There are two ways to access Gramene resources on the Internet. If you do not use Biobar, simply open your browser, type in the address bar, and press “enter”.
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4. Option 2: Access Gramene on Mozilla via Biobar
Get Biobar at
Option 2: Access Gramene on Mozilla via Biobar
If you use a Mozilla based browser, such as Firefox/Flock/Mozilla/Netscape or Seamonkey, you may have Biobar, a toolbar that provides access to major biological databases, bioinformatics tools and websites. From the left-most icon of Biobar select “Plant databases” and from that drop-down menu select “Gramene”. (You may also search Gramene directly through the Biobar search interface, although this does not give you access to Gramene’s power searches.)
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5. Date and Release # of current version of database. (Only on home page)
Quick search – general search of multiple modules plus website pages
Date and Release # of current version of database. (Only on home page)
Home Page
Gramene Calendar
News about the current release and the grass genomic community is listed here
Quick Start helps get you directly to where you want to go fast.
The Gramene Home Page
Release Number: At the top right of the home page you will see the database release number and date of release. This information will be needed for citing Gramene, and is found only on the home page. Any time you want to return to this home page, simply click on the Gramene logo at the top left.
Nestled between the top and bottom navigation bars you will find:
Search – The search box is easily accessible first thing on the website. You may select to search the whole website, or select a specific module to search. If your search takes a long time, try searching a single module. Also, consider the term you are searching. Browse Ontologies to find related terms you may also wish to search for. Wildcards can be used by entering “*” in your search. BLAST and GrameneMart are tools rather than data files, so they don’t appear in the search. And the two newest data modules – Diversity and Pathways – cannot be queried in a search from here, so if you are looking specifically for those types of information you should go directly to those modules. Also, for a more powerful individual module search you should go to the module of interest and use the search options and filters often available on those pages.
Questions and Tips: Each time you open the Gramene Home page, a helpful tip for using the site will appear to facilitate your use of the site. You may view all the tips by clicking on the associated link. Other links assist users through the FAQ, feedback and tutorials.
Quick Start: Quick links provide immediate navigation to commonly accessed pages. Short explanations here simplify your navigation. A brief introductory description of Gramene is given below this section.
What’s new: Along the right hand side of the home page are links to news items. Some news will be specifically about Gramene, such as the Gramene newsletter, release information and Gramene workshops. The featured news will also list community news of interest to Gramene users. There are also links to previous release notes, community news, and the Gramene Calendar.
Gramene Help and Tips give advice on using the site. Click “All Tips” for more pointers.
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6. Page Navigation www.gramene.org
(If some website features don’t work correctly,
try using a different browser)
Quick search, optionally select a specific database to search, enter a term to search for, and click on “search.”
Title identifies the page being viewed.
Click logo to return to Home page
The following items are available on every page:
The Gramene Logo is located at the upper left. Clicking on the logo from any page will return you to the Gramene Home Page.
Above the navigation bar is a quick search, where you can enter a term and either search all the databases, or select a single database. This can be a good place to start if you aren’t sure what you’re looking for, or just to get acquainted with Gramene. This simple search is available at the top of every page. If you don't know which database to use, Select "all" from the drop down menu.
There is a “feedback” button at the top right. If you are having problems with any page, select the feedback button from that page. It will reference the page you were on and provide a space for you to enter your question or problem. Be sure to provide your name and , or the feedback cannot be submitted or replied to. Questions from others are maintained in the mail archives.
On the far right of the top navigation bar is the “feedback” button. If you click here it will open a window for submitting a comment, question or error report to Gramene. It will reference the page that you were on when you clicked “feedback.” You will need to enter a valid in order to submit feedback and to get a reply from the appropriate person at Gramene.
Dropdown Navigation Bar (see next slides)
Easily accessible “Feedback” button on every page.
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7. Footer Click “Species” or seed images to link to species pages
Collaborators and funding sources are linked along the bottom
Provides an overview of everything on the site
At the bottom of every page is a consistent navigation bar. This provides links to the species pages, funding agencies,
The bottom navigation bar is the “species bar.” Click on “species” to go to the species home page, or click on a seed image to go to the corresponding specie page. The icons on the right side of the Species bar” represent the organizations that fund the Gramene project. Below the program are quick links to the Gramene home page, the site map, information about Gramene, and citation information.
Gramene purpose, history and people
Information about citing Gramene
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8. Searches
Gramene Modules and tools used to access the databases. See individual module tutorials.
Note that you are in the QTL module
The first item on the main navigation bar is “Search”. This is the entrance point to information in the Gramene database. The data is categorized into separate modules for searching purposes, and each module will have its preferred method for searching, as well as wild card options (if any). The best place to begin a search at Gramene is often in the module of what you want. If you want information on a marker, look in the markers module, if you want to learn about a protein, go to the proteins module. As you become more familiar with Gramene, you will find that most of the modules are interconnected, and you may move between modules as your search progresses. Each of these modules have their own tutorials.
The Genomes module has a genome browser that uses Ensemble technology to display genes, markers, expressed sequences and other information on the Rice-Japonica, Maize and Arabidopsis genomes. Sequences from other cereals – such as sorghum, barley and wheat - can be mapped on the rice genome, displaying colinearity. This module links to the Maps and Ontologies modules.
In the maps module you can browse or search for genetic and physical maps of rice and other cereal species. Become familiar with the menu here. You may search maps, features, or species. The CMap tool, from GMOD, is used for viewing maps and making comparisons between maps and showing colinearity between species. The matrix can help you determine which are the best maps for making comparisons.
In the markers module you may search markers based upon name, type or species; View its detail; Link to the maps, literature and ontologies databases.
In the QTL database you can search quantitative trait locus (QTL) from major cereal crops associated with traits, and link to maps, genomes, ontologies and literature. The power search allows you to include or exclude traits, species and chromosomes in your search.
The Gramene Genetic Diversity is a source of rice, maize, and wheat bio-information from/for evolutionary, domestication, association, and genetic diversity studies. It also links to the Gramene Markers DB.
In the Genes module you can learn about genes and alleles associated with important phenotypes and functions. This information links to the literature, ontologies, maps and genomes databases. You can also submit gene ontologies.
In the proteins database you may search to find a protein, it’s sequence, and associations, link to NCBI and SwissProt, or conduct a BLASTP query. “Proteins” links to the ontologies and literature databases.
In Pathways, AKA RiceCyc, you may search or browse the pathways to visualize how a gene, protein or compound affects the biochemical metabolism in rice. In order to get gene information, this module links back to the Genomes database.
The Ontologies database maintains several different ontologies, including the GO, PO, GRO, TO, EO and GR_tax. Ontologies help you to find key words for conducting a search in other modules, such as the QTL module. Link to genes, QTL, maps and proteins, or submit terminology to ontologies.
The literature database lists the literature that has been used in curation of the Gramene databases. Search by keyword or author, read the abstract, and link to on-line sources for publications.
BLAST is a tool used to search for DNA or peptide sequence similarities in order to align a known sequence with the complete genome.
GrameneMart is a data-mining tool that is still under development. It is a search tool that greatly simplifies searches by starting with a sequenced genome, and applying filters to remove extraneous information. Currently it allows you to search gene and protein information in Gramene. Further development will allow you to get information from the whole database through selected filters.
Each module has it’s own search page, and frequently there is also an advanced search option. These searches can be more powerful than the general search, but they will not search the whole database.
Each module has it’s own module-specific navigation bar below the main Gramene navigation bar.
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Module specific searches will search ONLY that module

9. Genomes Click Logo to return to the Home page See Genomes Tutorials
Select Genomes to access the genome browser.
Rice/Maize synteny views are available from either the rice or the maize genome pages.
Next to the search options you will find a link to the genomes. This is the same as the “genomes” link under search, but it provides quicker access to each of the species available in Gramene.
In addition to the datasets, Gramene hosts the sequenced genome assembly of Rice-japonica, and Arabidopsis, in addition to the FPC physical map of maize. The rice genome serves as the entry point for carrying out sequence based comparative genomics analyses with other grains. The Rice and Maize genomes have been aligned to show synteny.
Select a genome to view.
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See Genomes Tutorials

10. Species Select a Specie from the menu or the footer.
Select to change specie.
Each species page provides information in many categories
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11. Download data or software to install Gramene on your own machine.
Downloads
Download data or software to install Gramene on your own machine.
Gramene is a curated, free for use, web-accessible data resource for comparative genome analysis in the grasses. The database and the curated datasets are freely available for local use and installation. Gramene hosts only publicly available data, and some researchers download the database to incorporate their private data, or may be interested in only a single dataset from Gramene. Database releases occur 4 times a year, and local copies may enhance their control over layout changes.
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12. Resources Provides links to other websites of interest
Definitions of terms, abbreviations and acronyms used. Links to other on-line glossaries
Submit a gene or ontology term to the database
Links page of genetic newsletters for cereals
The Resources section is a major offering at Gramene. The Species pages provide specie, anatomy, taxonomy, production, nutrition and germplasm information for the major cereal species. There is also a summary page of Gramene data available for each species.
The Glossary at Gramene provides links to several online biological bioinformatics and biotechnology glossaries, as well as definitions to many of the terms found on the Gramene site.
There is a link for submitting Genes an ontology terms to Gramene here under resources.
The Resources page is our “links” page, with categories pertinent to genome sequencing, functional genomics, databases and bioinformatics, taxonomy, and plant breeding, among others.
The Newsletter link provides access to several genetics newsletters, database program newsletters, and other industry news.
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13. Click to access Gramene information and history.
About
Click to access Gramene information and history.
The About section provides information on Gramene history, personnel, collaborators, employment opportunities, and citation information, as well as contact information and the program Brochure. The link to Program Outreach lists workshops that have been done, and links to available exercises or presentations from these workshops.
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14. Help Gramene help docs and documentation
Searchable Frequently Asked Questions about Gramene, curation, and database modules.
E-Lists for discussion and for announcements
The “help” section provides links to help documents, tutorials, FAQs and workshop exercises in order to help you utilize the database resources, and information on rice gene nomenclature. There are also links to be able to ask questions of the Gramene developers or join the Gramene list-serves.
The Gramene Site map lists all major sections and pages of the website and offers a visual overview of resources. Help Documents, release notes, tutorials, FAQs and workshop materials help users to learn how to maximize their efforts with the database. Mailing lists offer opportunity for discussion with the Gramene developers, curators, and other users. Direct assistance is available from any page through the “Feedback” button.
Link to info on Rice gene nomenclature
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15. Email Gramene at gramene@gramene.org
Contact Gramene
Get contact info
Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene. or
This has been an overview of the Gramene website. I recommend becoming familiar with the site and the individual modules at your leisure, so that when you need information from the database you are able to retrieve it more quickly. You will find tutorials in various formats for each module. Please contact us with comments, questions and suggestions.
Gramene at
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