DARTS»SEARCH

Description

• 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.
• The GENica Marker Tools "DARTS" module allows storing the users' DArT^® genotype data.
• Select DARTS»SEARCH to search genotype information stored in DARTS.
• Search results can be downloaded in 2 different formats, a "Marker x Sample array" and a "Table View" that can be customised.
• Search results can be marked for future use by "tagging". Tags can be used as a way of grouping samples or markers in DARTS for future reference, to search for marker information in MARKERS»SEARCH or to mark data for deletion from DARTS.
• For details on how to upload genotype data, please refer to the section on DARTS»IMPORT.
• To browse the information available in DARTS, please refer to the manual section on DARTS»BROWSE.
• For details on how access to the data in DARTS is controlled, please refer to the manual sections on user groups.

Back to contents

Search DARTS

• A DARTS search involves three steps, illustrated on this screenshot of the DARTS»SEARCH interface:
  1. Entering search parameters: In the top left-hand corner of the DARTS»SEARCH interface, search parameters are entered and a search is launched.
  2. Choosing to display results from one or more searches: In the top right-hand corner, a "search history" table lists searches, their search parameters and number of "hits". A search's results can be viewed individually, or in combination with other search results. Searches can be combined with "AND", "OR" and "NOT"; operator precedence can be controlled with brackets.
  3. Viewing and managing search results: The actual search results are displayed on the lower half of the interface; these can also extend to extra results pagers. This results display can be customised. Results can be exported in their customised format and / or "tagged" for further use (e.g. for future reference or to delete data points).

Back to contents

Entering search parameters

• Use the following search options either individually or in combination to search the genotype information in DARTS.

Tag

This drop-down box gives you access to all the "DART Sample" and "DARTS" tags you have previously created.

Group

Use the drop-down box to select data belonging to one or all of your user groups.

Project

Use the drop-down box to select data belonging to one or all of the projects. Only projects belonging to the selected user group(s) and that contain DArT^® data are listed.

Service

Use the drop-down box to select data belonging to one or all of the Triticarte "Services" in a project. Triticarte assigns a unique "Service number" to every order they receive. If an order includes more than one plate, each plate is given the same "Service number". Only "Service numbers" belonging to the selected project(s) are listed.

Plate

Select the plate for which you would like to see DArT^® data. Only plates belonging to the selected "services" are listed.

Other

• Use the drop-down box to select a field you wish to search with a keyword.
• In the text box, enter a search string. As wildcards, use "%" (the percent symbol) for any number of characters (including zero characters); use "_" (the underscore symbol) for exactly one character.
• If more than one DARTS field is to be searched, click on the [ADD] link next to the text box. This will save your first selection and open a new "Other" search option to enter another field-specific keyword search.

Marker

Use the drop-down box to select only data for one of the markers used in a project. Only markers belonging to the selected plate(s) are displayed. To select alleles for markers that have a CloneID, but no DArT^® marker name yet, search the "Clone ID" field under "Other".

Allele Score

DArT^® allele scores can be "1", "0" and "-" (for missing). If you want to select only samples that have a specific allele score, you can enter it here.

• To launch a search, hit the SEARCH button.

Please note: Search parameters are combined with "AND", i.e. only entries that meet all the criteria are selected. To combine search parameters with "OR" (meaning that entries are selected if they meet at least one of the search criteria), use the "COMBINE SEARCHES" option described in the next section.

• Searches are listed in the "Search History" table on the top right-hand corner, where the number of "hits" for each search is listed alongside the search parameters used and the search number.
• Select to view the results for a search, or carry out other searches to combine with the first search. See the next section for details on how this is done.

Back to contents

Viewing results from one or more searches

• All searches are given a number and recorded in a "Search History" table, where the search number, hits, and search parameters are listed. (See the top right-hand corner of the DARTS»SEARCH interface.)
• Click on the [REMOVE] link next to a search to delete it from the "Search History" table.
• Click on the [VIEW RESULTS] link next to a search to see the DARTS entries for that search only.
• Use the "Combine Searches" option to combine and display results from more than one search:
  1. Enter the search numbers and how you wish to combine them in the "Combine Searches" textbox. Searches can be combined with the Boolean operators AND, OR, NOT; operator precedence can be controlled by using brackets.
     • AND: When searches are combined with AND, only DARTS entries that meet the search criteria of all the combined searches are displayed ("intersection").
     • OR: By combining searches with OR, all the entries meeting the search criteria of any of the combined searches are displayed ("union").
     • NOT: By specifying e.g. "1 NOT 2", only entries selected by search "1" that are not also selected by search "2" are displayed ("exclusion").
     • Operator precedence:
       • Default operator precedence is "AND" before "OR". The entry: "1 AND 2 OR 3" would therefore be interpreted as meaning: "(1 AND 2) or 3" (i.e.: 'Display all the entries that searches "1" and "2" have in common, as well as all the entries from search "3".')
       • Use brackets to overwrite the default operator precedence, e.g. writing "1 AND (2 OR 3)" would be understood to mean: 'Display all the entries that search "1" has in common with either search "2" or search "3".'
  2. Hit the VIEW RESULTS button to combine searches and display results.

Back to contents

Managing search results

• After search parameters have been entered and one or a combination of searches have been selected by hitting [VIEW RESULTS] next to a search or the "Combine Searches" textbox, DARTS entries are displayed on the lower half of the DARTS»SEARCH interface.
• 'GENica Marker Tools' allows a choice of display options that can be further customised. DARTS search results can be exported in their customised format.
• Search results can be tagged for downstream purposes.

Back to contents

Change the way DARTS search results are displayed and exported

• A drop-down box at the top right-hand side of the DARTS search results allows selecting different "views": The "Matrix view" and the "Table view".
• When search results are exported, the active display setting determines the export format and which fields are included in the downloaded file.

Back to contents

The Matrix view

• The "Matrix view" is the default view for search results. Marker names are arranged across the top of the table, sample names down the left-hand side.
• To prevent the creation of Sample x Marker arrays that are too large to navigate conveniently in a web interface, only a limited preview of the data is shown to allow assessing a sample of the query results.
• To see the whole data set, the SamplexMarker table has to be exported by clicking on the [DOWNLOAD RESULTS] link.

Please note: If the Sample x Marker array has more than 256 columns, please also refer to the section on spreadsheet viewers without a 256-column limitation.

• If all the search results are to be tagged for further use, select the [TAG ALL RESULTS] button and proceed as described in the section below on tagging. If you wish to tag individual DARTS entries, switch to the "Table view" first.

Back to contents

The Table view

• Switch to the "Table View" by selecting it from the drop-down box at the top right-hand side of the DARTS search results table.
• All the DARTS entries matching your query are listed. The information can be displayed on several results pages. Use the [first], [prev], [next] and [last] buttons to move between pages, or type a page number into the "page" text box, then hit "enter".
• Click on a column header to sort the "Table view" by that column.
• Click on the [SELECT COLUMNS] above the results table to customise the "Table view" in 'GENica Marker Tools' OPTIONS:
  1. Change the number of lines displayed on each page.
  2. Select the columns to be displayed in the "Table view" by ticking / unticking the boxes under "DARTS Table Fields". All the fields from the original DARTS import file are available, plus extra fields created within 'GENica Marker Tools' (e.g. "User Group", "Project").
• "Tag" search results for further use as described in the section on tagging.

Back to contents

Export DARTS search results

• Select the [DOWNLOAD RESULTS] option to download data in its current format.
• The export file format is a delimited text file; choose from tab-delimited *.txt or comma-delimiated *.csv in 'GENica Marker Tools' OPTIONS.
• The downloaded results file can be opened with a text editor or a spreadsheet viewer. Please refer to the section below if a SamplexMarker table with more than 256 columns has been exported.

Back to contents

TAG DARTS search results

• "Tagging" a marker or a sample in 'GENica Marker Tools' is similar to adding a record to a "clipboard" or a "marked list" and saving this "clipboard" / "marked list" for future reference.
• Although a tagged entry remains e.g. in its "DARTS project" or "marker set", it now also forms part of a tag. This allows grouping entries from different projects, marker sets, user groups, runs, etc., without having to save new "copies" of these entries in the database.
• Existing tags can be accessed and edited through the 'GENica Marker Tools' TAGS mode of function.

Back to contents

"DARTS Tags" versus "DARTS Sample Tags"

• When tagging DARTS entries, select "DARTS Sample Tags" to tag samples and "DARTS Tags" to tag markers and the related allele values in a data set.
  • "DARTS Sample Tags":
    • Tag DARTS search results with a "DARTS Sample Tag" to mark the samples selected by the search for future reference. This can be useful e.g. to quickly retrieve samples with a particular idiotype, once they have been selected by combining multiple searches in DARTS»SEARCH.
    • Tag DARTS search results with a "DARTS Sample Tag" to delete the selected samples from a DARTS dataset. This allows deleting one or more individual sample(s) from several runs, projects or even whole groups without having to go through every run's list of samples one at a time.
  • "DARTS Tag":
    • Tag DARTS search results with a "DARTS Tag" to mark its markers for future reference. A DARTS Tag can be opened within the MARKERS»SEARCH interface to access marker-specific information such as GenBank accession or a marker's origin. A DARTS Tag can be opened within the DARTS»SEARCH interface to access which samples were genotyped with the tagged markers and what allele values were recorded.
    • Tag DARTS search results with a "DARTS Tag" to delete its markers from a DARTS dataset. This allows removing allele records for one or more marker(s) from individual samples or from all the samples in a particular run or even from all the samples assessed with the marker(s) in a whole project.

Back to contents

TAG all search results

• Click on the [TAG ALL RESULTS] link to tag all the records selected by "view results". This will select all the hits for the selected search(es), regardless of whether results are displayed over several pagers or not actually visible in the "SamplexMarker" results preview.
• A "Tag Search Results" interface opens, where a new tag can be created or an existing tag can be selected. Be sure to select the correct "tag type" ("DARTS Tag" or "DARTS Sample Tag") for the tag's purpose.
• Click SAVE to begin tagging. After tagging is complete, the TAGS»DARTS or the TAGS»DARTS SAMPLE interface opens, depending on the chosen tag type, where a tag can be reviewed, edited or deleted.

Back to contents

TAG individual records

• To tag individual records, switch to the "Table view" first.
• Check the boxes next to the records to be tagged.
• At the right-hand side above and below the DARTS»SEARCH results pane is a TAG button next to a "Tag" drop-down box. Choose "New Tag" or the name of an existing tag from the drop-down box, as appropriate, and click on the TAG button.
• If creating a new tag, specify the tag name and tag type, making sure to select the tag type that is correct for your intended purpose.

Back to contents

Spreadsheet options for data arrays with more than 256 columns

• Arrays downloaded from GENica Marker Tools can be wider than the 256 column limitation existing in Excel 2003 or earlier.

IMPORTANT: If Excel 2003 or earlier versions are used to open a file with more than 256 columns, extra columns are lost. These files can be opened without losing data in one of the following applications:

• Excel 2007 (16,384 columns x 1,048,576 rows).
• "Corel Quattro Pro X3", available as part of the "Corel WordPerfect Office X3" package. Settings can be changed to allow up to 1,000,000 rows and 18,278 columns, see [1] for information and a trial version.
• "VisualStat" worksheet properties can be formatted to have up to 2,000,000,000 rows and up to 2,000,000,000 columns, see [2] for information and a trial version.
• A basic spreadsheet is available as part of Microsoft's Office Web Components (up to 18,278 columns and 262,144 rows, see [3] for information).
• "Gnumeric" can be compiled to have arrays with over 256 columns. Please refer to [4] for general information and to its FAQ site for advice on how to set maximum column and row numbers.

Back to contents

Links to other user manual pages

I'd rather try the tutorial...

• Get started with the GMT Tutorial
  Log in to 'GENica Marker Tools'