MARKERS»SEARCH

Description

• Select MARKERS»SEARCH from the 'GENica Marker Tools' main menu to search the MARKERS Table.
• Links to the GENica CMAP installation allow convenient searches for maps featuring a molecular marker, see details below.
• For a marker of interest, detailed information, e.g. on primer sequences and peak appearance, can be found by using the VIEW option or by switching between different DISPLAY options.
• The MARKERS Table contains information for the different types of markers supported by GENica Marker Tools. Currently, these are SSR, EST-SSR, INDEL, DArT^® and SNP markers:

"General" and "Multiplex-ready^TM" Microsatellite (SSR) Marker Information

• The MARKERS Table can be used to store and edit a user's own sets of microsatellite markers, for example to allow binning markers with user-defined, germplasm-specific allele size ranges, or to store information on markers that are not part of the Multiplex-ready^TM Technology. Please refer to the section below on editing and deleting markers in the MARKERS Table and to the manual sections on MARKERS»SETS, ADMIN»MARKER DB IMPORT and MARKERS»IMPORT for details on creating and managing custom marker sets.
• The MARKERS Table contains constantly up-dated and centrally curated information on multiplex-ready^TM SSR markers created by Matthew Hayden in the marker sets called Wheat and Barley (formerly available in the MRT Markers Database).
  Last updated: 15 February 2007, MRT Marker DB version 5.0.
• The allele size information in marker sets Wheat and Barley can be used to "bin" wheat and barley "multiplex-ready^TM markers. See also the section on how to BIN MARKERS for further information. This allele size data was generated using eight genetically diverse varieties:
  • The varieties used for barley were Alexis, Chebec, Clipper, Harrington, Haruna Nijo, Sahara 3771, Sloop and WI3408.
  • The varieties used for wheat were Barunga, VPM Cook, Chinese Spring, Gabo, WI7984 (a synthetic hexaploid), Norin10, Olympic and Opata85.
  • In our experience, the allele size range reported for each published marker is generally sufficient to avoid allele overlap in domesticated germplasm. However, it should be realized that some markers may have allele sizes outside the expected range in certain genetic backgrounds, which may result in marker allele overlap.
• Marker information in marker sets Wheat and Barley is equally used in the "Automated Designer" macros that help design marker screening and genotyping experiments with MRT markers (please refer to the section on FILES»LIST for details on downloading and using the "Automated Designer" macros, or read the step-by-step instructions in the GMT Tutorial).

Single Nucleotide Polymorphism (SNP) Marker Information

• The MARKERS Table can be used to store and edit a user's own sets of SNP markers. Please refer to the manual sections on MARKERS»SETS and ADMIN»SNP MARKER DB IMPORT for details on creating and managing custom marker sets.
• Publicly available wheat and barley SNP markers are being adapted by Matthew Hayden for analysis on the Luminex platform after "FlexMAP microsphere^®"-based allele-specific primer extension (ASPE) assays. Data for these is stored in marker set SNP Markers (MPBCRC:public;mhayden)
  • Barley SNP markers were originally reported in the Barley SNPDB, developed at the Scottish Crop Research Institute (SCRI).
  • Wheat SNP markers were originally reported in the NSF SNP database.

DArT^® Marker Information

• DArT^® (Diversity Arrays Technology) markers were developed by the people at Diversity Arrays Technology P/L; DArT^® genotyping services are offered to the wheat and barley community through their subsidiary, Triticarte P/L. Please refer to these companies' websites for information on the technology and on available services.
• When complete DArT^® marker information for wheat and barley markers is released from Triticarte, it will be displayed here to allow crossreferencing general marker information and DArT^® genotype data in DARTS.

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Search the MARKERS Table

• Use the "drop-down" boxes individually or in combination to search the MARKERS Table.

Marker Set

• This drop-down box allows selecting markers by marker sets or by tags. All the sets and tags a user has access to are displayed.

• Marker Sets:

• Markers are always grouped in marker sets. The user group to which a marker set belongs, its access level and the name of the user who has imported a marker set are displayed in brackets. Please refer to the section on MARKER SETS for more details.
  • Select marker set Barley or Wheat to find up-to-date information on "multiplex ready"^TM markers for these two cereals. These marker sets are created and curated by Matt Hayden.
  • Select marker set SNP Markers (MPBCRC:public;mhayden) to find information on SNP markers adapted for "FlexMAP microsphere"-based ASPE (allele-specific primer extension) assays by Matt Hayden.

NOTE: The MARKERS Table contains both centrally curated data and user-provided marker information. For the marker sets that have been created by general users, some or even most of the information in the "View Marker" interface and in the MARKERS Table may be missing. While the information in Wheat, Barley and SNP Markers (MPBCRC:public;mhayden) has been prepared with the utmost care, the GENica disclaimer always applies.

• Marker Tags:

• If markers have been "tagged" in MARKERS or in the GEMDB, SNPDB or DARTS mode of function, these tags can be selected from the "Marker Set" drop-down menu. Please also refer to the section on TAGS to find out more.

Prefix

Use the Prefix drop-down menu to search for markers by the prefix of their published name.

Type

This drop-down menu allows searching for markers of one of the following types:

• EST-SSR (microsatellite markers derived from expressed sequence tags)
• SSR (microsatellite markers)
• INDEL (insertion / deletion marker)
• STS (molecular marker derived from a sequence tagged site)
• DArT^® ("Diversity Arrays Technology" markers, see also http://www.triticarte.com.au/)
• SNP ("Single Nucleotide Polymorphism" markers)

Quality

The drop-down menu allows filtering for markers by their quality score. Marker quality scores for multiplex-ready^TM markers were assigned according to the system described in Stephenson, et al. (1998) Theoret Appl Genet 97, 946.

Field

Specify which of the MARKERS Table fields to include in a string search.

Search Strings

• Wildcard characters: Use '_' ("underscore" character) to match any single character. Use '%' ("percent" character) to match an arbitrary number of characters, including zero characters.
• Use ',' ("comma" character) to separate a list of search terms. The comma functions like the boolean OR separator and can be used to separate marker names when searching for information on a list of markers. See also the search examples below for another example of how commas can be used to separate other types of search strings.
• When entering marker names in the search field, 'GENica Marker Tools' will usually recognise them as a prefix followed by a number. To give an example, the search term "hv3" is equivalent to entering search terms "hv03", "hv003", "hv0003"; search term "AB9307" is equivalent to "AB009307".

IMPORTANT: If the "search string" field is left empty, no records will be selected. Be sure to enter % as a search string if you want to select all the data available in the MARKERS Table or in one of its subsets.

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Search example: Selecting barley MRT markers by chromosome location

• Select Barley from the Marker Set drop-down menu
• Select CHROMOSOME from the Field drop-down menu
• Type in a search string, e.g.

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Search example: Selecting wheat MRT markers by chromosome location

• Select Wheat from the Marker Set drop-down menu
• Select CHROMOSOME from the Field drop-down menu
• Type in a search string, e.g.

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Browse the MARKERS Table

• Browse between pages of information with the [first], [prev], [next] and [last] buttons.
• Rearrange the marker information by clicking on any column header that you wish to sort the data by.
• To change the number of lines displayed per page or the column headings displayed in the "Custom View", edit your preferences (please refer to the section on OPTIONS).

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Change the way the MARKERS Table is displayed

• A drop-down box at the top right-hand side of the MARKERS Table allows selecting different "views".
• The table below show which MARKERS Table fields are available in the different display views.
• Click on a field name for a description.
• The "Custom View" is customised through OPTIONS.
• Please note that instead of displaying the beginning and end of the different allele ranges in separate rows, the "Custom View" and the "Import / Export Format" view display them in different columns.
• When search results are exported, the currently active display setting determines which fields are included in the downloaded file.

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The MARKERS table fields available in the different "View" settings
(Click on the boxed arrows next to a column header to change the table's sort order. Click on a field name for a description.)

¹Please note: By selecting the "Re-engineered SSR Markers View", only markers that have been redesigned to create "spatial variants" are displayed. Accordingly, if none of the markers selected with the search options in MARKERS»SEARCH is a "re-engineered SSR marker", no markers are displayed in the MARKERS Table.
²"Custom View" fields are selected in OPTIONS.
³The "Import/Export Format" corresponds to the format required for the "Automated Designer macros" and for MARKERS»IMPORT. Export SSR markers in this format for bulk off-line editing of allele size ranges (e.g. in a spreadsheet program) and re-import into a custom marker set.
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Information in the MARKERS Table

• The MARKERS table fields are described in detail on this webpage. Please also refer to the section on display options for information on which of these fields are available in the different view options.

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Export information from the MARKERS Table

• After selecting markers and a view that displays the fields of interest, hit the [DOWNLOAD RESULTS] link.
• The exported file will have entries for all the selected markers.
• The same fields as in the currently active "view" (see section above) are exported.
• To export MRT^TM markers in an "Automated Designer"-compatible format, choose the "Import/Export Format" view.
  This is also the format to be used if a template for MARKERS»IMPORT is required.

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TAG markers

• After selecting markers in MARKERS»SEARCH, you can "tag" them for future reference or to pass the selected markers on to BINNER»MRT TAGS (multiplex-ready^TM markers) or to BINNER»SNP TAGS (SNP markers adapted to "Flex-MAP microsphere"-based OLA and ASPE assay on the Luminex platform).
• Markers can be given a new or an existing tag. The latter option allows grouping markers that cannot be easily displayed together in a single search.

TAG all search results

• Using the [TAG ALL RESULTS] option will tag all the search results on all the results pages, not just on the currently displayed page.
  1. Click on the [TAG ALL RESULTS] link situated at the right-hand side above and beneath the MARKERS table.
  2. A "Tag Marker Search Results" interface opens, where you can either enter the name of a new Marker Tag you wish to create, or select one of the existing Marker Tags.
  3. Click SAVE after you have made your selection.
  4. The TAGS»MARKERS interface opens, where all your Marker Tags are listed. Use [DELETE TAG] to remove a Marker Tag, [EDIT MARKER TAGS] to "untag" markers you do not want to include in a Marker Tag. The [VIEW MRT MARKERS] opens the Marker Tag in the MARKERS»SEARCH interface.

TAG individual markers

1. "Check" the box next to the marker to be tagged.
2. Use the "Marker Tags" drop-down box, situated at the right-hand side above and below the MARKERS Table, to choose an existing tag or "New Tag".
3. Click on the TAG button next to the "Marker Tags" drop-down box.
4. If "New Tag" had been selected, the "Tag Marker Search Results" interface opens, where the name of a new Marker Tag can be entered, or one of the existing Marker Tags can be selected. Click SAVE after making your selection.
5. The MARKERS Table is displayed, with a message saying: "Markers have been tagged".
6. Select TAGS»MARKERS to view, edit and delete Marker Tags.

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The CMAP link

• CMAP is a web-based tool that allows users to view and align genetic and physical maps. Please also refer to the CMAP user tutorial for instructions on how to use CMAP.
• Click on the [CMAP] link next to a marker to start a "Feature Search" of the GENica CMAP Installation with this marker. The result is displayed in a new browser window.
• If maps with this molecular marker exist, details are displayed in a table in the CMAP window.
• Click on the [View on Map] link in the CMAP feature search results table to open a browser window with a graphic representation of the map with the marker highlighted on it. (To see other features on a map, you may have to select: Show Additional Options Menu » Show labels: All, followed by: REDRAW MAP.)

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The VIEW option

• By selecting the [VIEW] button on the far right of a marker, the "View Marker" interface opens with all the available MARKER table entries for that marker.
• The [VIEW] option allows to find detailed information for one marker at a time. To see these details for several markers at a time, consider switching between the preset display options.

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The EDIT and DELETE Options

• Edit and delete options exist for markers in marker sets belonging to the user. Group administrators have edit and delete rights to markers that were created by any user in the group(s) they administer.
• Select [EDIT] next to a marker to open an "Edit Marker" interface where the marker's name, its marker set and the existing allele size ranges can be edited. Click on the ADD LOCI button to add extra allele size ranges for a marker, specifying the minimum and the maximum allele size in bp.

NOTE: To edit the information for a marker in a gemdb marker set, you have to specify a binner marker set on the "Edit Marker" interface. If you do not have access already to a binner marker set, you can create one by using the MARKER SETS ADD option.

• Select [DELETE] next to a marker that you wish to delete from a marker set. A "Delete Marker" interface appears, prompting to confirm or cancel this action.

NOTE: A marker can only be deleted if no allele records exist for this marker in GEMDB.

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Links to other user manual pages

I'd rather try the tutorial...

• Get started with the GMT Tutorial
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