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Use the "Markers Search" tool to search for markers. When you first visit this tool, you are presented with a simple form for searching the marker database. 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. Below the search examples is a summary of the number of markers by each type with a link to "Search" for those markers.
To conduct a search, you can enter any number of 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)"). You may use the wildcard character "*" 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.
To further refine your search query, you may specify a marker type (e.g., "RFLP") and/or a species (e.g., "rice"). Each search parameter can be used alone or in conjunction with any other parameter. 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.
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, the marker type (or "Undefined" if not known), and the number of times the marker has been mapped to a map available in Gramene's Maps module. The results table may be sorted by clicking any of the column headers except for the synonyms. To view the details on the marker, species, or marker type, simply click on the marker name, species name, or marker type.
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.
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"), but every page will include the following:
| Marker Name: | The marker's primary name. |
|---|---|
| Synonyms: | Any known alternative names. |
| Type: | The marker's type. Click on this to view the "marker type details" page. |
| Species: | The species from which the marker was derived. Click on this to view the "species details" page. |
| Germplasm: | The germplasm from which the marker was derived (or "N/A" if not available). |
| Mappings: | 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. |
| Genome Positions: | Any positions found in Gramene's genome browser for the marker. |
| 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. |
| Images: | Any available images of the marker. |
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 a particular type.
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 of a particular type. In addition, any map sets linked to the species are shown. The map sets may be ordered by their type, name, or the number of maps they contain. To view the details of a map type or map set, simply click on the name in the table.
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.
The map set details page lists the name of a map set, along with its species, type, and accession ID in Gramene's Maps database. Choosing the species or map type will take you to the Markers database's details pages for those objects, while clicking the Maps accession ID will take you to Maps' "map set info" page for the map set. Below this, you will find a table showing the 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.
The map details page shows the map's name and the species, type, and name of the map set to which it belongs. The start and stop positions of the map are shown as well as the Maps accession ID which is hyperlinked to the Maps "map details" page. Below the map's information are shown 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.