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Gramene Markers Database Help Document

Markers search/browse options

A. Quick Search

• From the markers home page, enter a keyword into the "Quick Search" Box, and click on the search icon. Immediately below this form are some examples of what you could search for. Clicking on any of these search examples will initiate a search for that example and return the results.
• You can enter multiple marker names in the "Marker Name" search box; use commas or spaces to separate the names. If you are searching for a marker with a space in the name you must enclose the entire name between double quotation marks (e.g., "C742 (K)").
• Use "*" as a wildcard to subsitute for zero or more of any character in the search string (e.g., "RM*" will search for all marker names that begin with "RM"). If you simply submit the search form without supplying any parameters, a search for "*" (i.e., all markers) is performed.

B. Markers Search

• Browse by Marker Type

• Text search

  • Search terms as discussed above in Quick Search.
  • Optionally, to further refine your search query, you may specify a marker type (e.g., "RFLP") and/or a species (taxonomy) (e.g., "rice"). For "taxonomy" you may enter any species or species synonym (i.e., rice, oryza, oryza sativa).

  For instance, you may wish to search for all markers with a name starting with "RM," all rice markers (Oryza sativa), all SSR markers, or all of these conditions.

C. Browse Map Sets

Quick Search and Markers Search Results

After performing a searching, the results page will indicate how many, if any, markers were found. The parameters supplied to the search will be summarized in text, like Search results for all SSR markers matching "RM*."

If no markers are found, this will be indicated. If your search did not use a wildcard ("*"), a new search will be suggested using one.

If the search is successful, you will see one of two pages. If the search only returns one marker, you will be taken immediately to the marker's details page (see below); otherwise, the number of markers found will be indicated along with the current subset being displayed (e.g., "Markers 1 to 25 of 839.").

Click the "Previous" and "Next" links (when available) to move by one page through the result set. You may also enter a page number directly and click the "Page" button to jump directly to that page.

The table of search results shows columns that indicate the marker's primary name, any known synonyms, the source species, and the marker type (or "Undefined" if not known). The results table may be sorted by clicking any of the hyperlinked column headers. To view the details on the marker, species, or marker type, simply click on the marker name, species name, or marker type, respectively.

To download the results of a search, click the "Download Data" link at the bottom of the results table. This will return a tab-delimited dump of the entire result set (i.e., not just the subset currently being viewed). The fields in the dump include the same fields as the table view as well as "marker_id," the Gramene accession ID.

• General Information Accessed from the search results page by clicking on a marker name. A marker's details page lists all the data available to Gramene on a given marker. Some of the fields will vary among the different marker types reflecting the appropriate attributes (e.g., "forward/reverse primers" or "overgos"),
  • ID
  • Marker Name: The marker's primary name. When clickable, it links to another database within Gramene, such as QTL or Genes, or to an external database, such as GenBank for mRNA, for more information from that resource.
  • Synonyms: Any known alternative names.
  • Type: The marker's type. Click on this to view the "marker type details" page.
    • The marker type details page shows whatever details are known about a given marker type, such as its name, a description, and possibly some cross-references. A link is provided to allow you to easily search for all the markers of that particular type.
  • Species: The species from which the marker was derived. Click on this to view the "species details" page. Click on the GR_tax ID to go to the Taxonomy Ontologies at Gramene.
    • The species details page shows whatever details are known about a given species, such as its name, a description, and possibly some cross-references. A link is provided to allow you to easily search for all the markers or to view the maps for that species.
  • Germplasm: The germplasm from which the marker was derived (or "N/A" if not available).
  • Analysis
  • Description
  • Other - other categories that may pertain only to specific marker types.
    • Genbank Accession - SSR
    • GenBank GI and Genbank Version - GSS, mRNA - links to GenBank
    • Gene Symbol - genes
    • Trait Name - QTL
    • TO Term - QTL
    • Published Symbol
    • Gene Model - Gene Prediction - links to Genomes
• Source/Library
• Details
• Database Cross-references: Any cross-references, e.g., to Gramene's Literature database or to a GenBank sequence accession. If a cross-reference has a URL associated with it, then the cross-reference's value (e.g., a GenBank accession) will be hyperlinked to the appropriate source.
• Sequences
• Map Positions: The maps on which the marker can be found. Several of the fields in the "mappings" are hyperlinked to searches. Like "Species" and the marker's "Type" above, you can click on the "Species," "Map Type," "Map Set," and "Map" fields to view the details for each object. The name of the marker in a given mapping is shown in the "Name" column along with its start position and stop, if available. The "View on Map" and "Feature Details" links take you out of the Markers database and into the Maps database.
• Associations
• Images: Any available images of the marker.

Browse Map Sets Results

• Map Set Details
• Species
• Map Type - The map type details page shows whatever details are known about a given map type, such as its name, a description, and possibly some cross-references. In addition, all the map sets associated with the map type are shown. The map sets may be sorted by their species, name, or the number of maps they contain. To view the details of a species or map set, click on the name in the table.
• Map Set Name
• Description
• Published on
• Distance Unit
• CMap Map Set Accession - accession ID in Gramene's Maps database.
• Database Cross-References
• Mapsthe maps contained in the set. The maps may be sorted by their name or the number of markers mapped to them. To view the details of a map, click on its name in the table.
• Map Name -
• Species -
• Map Set Name -
• Map Type -
• Start Position -
• End Position -
• CMap Map Accession - the Maps accession ID which is hyperlinked to the Maps "map details" page
• Mappings by type - Types of markers on the map, linked by type to marker type detail. Restrict Mappings link will limit the next section (mappings) to show only that marker type.
• Mappings - any mappings of markers to the map. The markers may be sorted by their name, type, species, start or end positions. To view the details of any marker or its type or species, click on the name in the table.
• Mappings by Type
• Mappings by Map and Type

Other Resources

SSR Markers Resource	Links to the SSRIT Tool, the Panel of 50 standard SSR markers used by the Generation Challenge Program for rice diversity analysis, the Table of SSR Primers from McCouch et al. (2002), Supplementary tables from IRGSP (2005) publication, and other references and downloadable information.
Tutorial	More in-depth than the help pages, use the tutorial for an exaple of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency.
FAQ	Frequently Asked Questions - see what questions users have asked, and get the developers' answers.
Release Notes	For more information about the most recent release.

Feedback

• Please submit suggestions or questions to the Gramene team by either using the "Feedback" link at the top of the Gramene pages or by going to the following URL: /db/feedback/send_feedback?refer_from=/rice_mutant/index.html
• If you find any inconsistencies or mistakes, please communicate them to us by clicking on the "feedback" link. Your suggestions and feedback are highly appreciated by the Gramene staff.

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