Welcome to the Markers Database Tutorial Gramene v. 26 Welcome to the Markers Database Tutorial The Markers Database will allow you to locate a specific marker based upon marker name, marker type or species. Once identified, you will be able to view marker information, including ID, germplasm and genome positioning, as well as get marker-type specific information. Markers also link to the Maps, Literature and Ontologies Databases. 2/4/2019

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. 2/4/2019

Click here to open Markers Page Gramene Home Page Click here to open Markers Page On the Gramene Home Page (www.gramene.org) click on “Markers” on the upper Gramene Navigation Bar to open the Markers Home Page. 2/4/2019

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. 2/4/2019

Markers Home Page Use “Quick Search” to find a marker name or click on “Markers Search” for more advanced search options (see next slide). 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. “Help” documents for assistance Release Notes describe additions, updates, and changes for the latest release of the database. 2/4/2019

2. To refine search, specify a marker type and/or a taxonomy (species) 2. To refine search, specify a marker type and/or a taxonomy (species). For taxonomy use common or scientific name. Markers Search 1. Type marker name. Use * for wildcards. 3. Click “search icon.” Or Click to run sample searches. Clicking on “Search” lets you search for markers of that type. 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, all SSR markers, or all of these conditions. 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. These tables show a breakdown of markers in the database by marker type. Clicking on a marker type lets you view a definition of that marker type. 2/4/2019

Marker Search Result Title identifies parameters of the search. There are 146 results for this search. Click on linked column titles to sort results by that column. Click on a marker name to view its details (see Slide 10). Search results include marker synonyms. If you don’t know the name of a marker, you may search on its synonym. Click on species or type for more info on that species or marker type (Slides 7-8) After performing a search, 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 CMap comparative map viewer. 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. Use Download link at bottom to view a tab-delimited file of entire result set (see Slide 9). 2/4/2019

Species Detail Title identifies parameters of the search. Taxonomy Links to Ontologies Database. See Ontologies Tutorial Click to search for all map sets linked to the species. 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. Click to search for all markers linked to this species. 2/4/2019

Marker Type Detail Title identifies parameters of the search. Marker type detail shows what is known about a given marker type, such as its name, a description, and possibly some cross-references. Click to search for all the markers of this particular type. 2/4/2019

Marker Detail Title identifies parameters of the search. Click to open GenBank record. The germplasm from which the marker was derived, if available. 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. Info may vary by species. 2/4/2019

Source Library When available, this information will be posted here. Name links to source library page in markers, Ontologies link to Ontologies database. 2/4/2019

Detail SSR mRNA RAPD QTL SSR Primer Pair FPC EST Cluster Marker details vary with marker type and data availability. Here are some examples. RAPD QTL SSR Primer Pair FPC EST Cluster 2/4/2019

Database Cross References Lists references available in Gramene Literature database related to this marker. Links to reference detailed info. 2/4/2019

Sequences When appropriate and available, DNA sequences will be listed in their own section, with a link to BLAST. 2/4/2019

Mappings These links go to the Maps module, where you can get more information on this marker. See Maps Tutorial. 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. Click for Map Set info and view a list of all markers on this map. (As in Slide 18) 2/4/2019

Associations The basis of this association. Other markers associated with this marker. Click for marker info 2/4/2019

Images Title identifies parameters of the search. (note different example) If available, PCR images will be here. 2/4/2019

Browse Map Sets Browse or filter map sets by map type or species. Select hyperlinked headings to sort table by that column. There are 220 map sets in Gramene. You may search them by map type and species. Maps are grouped by type, then by species. Click for Map Set info. (See next slide) 2/4/2019

Browse Map Sets – Map concepts Any item that is positioned on a map is called a feature – also known in Gramene as a marker or a mapping. Feature (marker) types are shown on Slide #5. A map is a linear array of interconnected features. This could represent a single linkage group in the case of a genetic map, or a single contig for physical maps. Related maps are grouped into map sets. Generally, these are the result of a particular study, such as the set of linkage groups produced by a genetic mapping study. 2/4/2019

Map Set Info from Markers db The markers module contains genomic data for mappings. However, in order to view it as a visual map, this data must be exported to CMap and the Map viewer. Click to view this Mapset’s CMap data. This is the information available for the mapsets. Click on a category to expand it (next two slides) 2/4/2019

Click mapping type for a definition. Mapset data Crossreferences link to other databases – such as Gramene’s literature module, or to Graingenes. A Mapset consists of a series of related maps, in this case one for each chromosome. Clicking there will take yoy to the Map data, similar to the current view but for a single map rather than a mapset. Click mapping type for a definition. 2/4/2019

Mapset data Click Mappings Number for a clickable list with marker name, type, species, start, stop and link to feature information in CMap (see Maps/CMap tutorial).. 2/4/2019

SSR Markers Resource Use the SSRIT to search for repeats of your own data. (see slide 23) Click to view a panel of 50 common SSRs (see slide 24) Click to view this table of SSR Primers. (see slide 25) Get citation information, or link to the original article. 2/4/2019

SSRIT Select group length Select number of repeats Enter sequence in FASTA format 2/4/2019

50 standard SSRs Users may access this data from the SSR Resources. Markers with an asterisk represent a panel of 30 (not a wildcard as in a search). Click to access marked detail information. 2/4/2019

Table of SSR Primers from McCouch et al. (2002) The table is extremely large. Please be patient while it loads. This is the html table. You should select the tab-delimited file if you want to save it to your computer to put in a spreadsheet. 2/4/2019

Help Help files help the user to conduct a search, defines the available information from the module, and links to other help resources. 2/4/2019

Tutorials You may select between a powerpoint version or a pdf version of the tutorial. Navigate to other tutorials. Download free software to view tutorials. 2/4/2019

FAQs Search FAQ Feedback: Submit a question to Gramene Click questions to expand or collapse an answer

Email Gramene List-serve at gramene@gramene.org 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