Gramene v 26 Welcome to the Markers Database

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.

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. 2/22/2021 2

Gramene Home Page Click here to open Markers Page

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. 2/22/2021 4

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

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

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

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. Click to search for all markers linked to this species.

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 crossreferences. Click to search for all the markers of this particular type.

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

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

SSR Detail RAPD Marker details vary with marker type and data availability. Here are some examples. QTL SSR Primer Pair FPC EST Cluster m. RNA

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

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

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

Associations The basis of this association. Other markers associated with this marker. Click for marker info

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

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)

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. 2/22/2021 19

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)

Mapset data 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. Crossreferences link to other databases – such as Gramene’s literature module, or to Graingenes.

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). .

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.

SSRIT Select group length Select number of repeats Enter sequence in FASTA format

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.

Table of SSR Primers from Mc. Couch 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.

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

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.

FAQs Search FAQ Feedback: Submit a question to Gramene Click questions to expand or collapse an answer 2/22/2021 29

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 2/22/2021 30