SNPDB»SEARCH

Description

• SNPDB contains user-provided Single Nucleotide Polymorphism genotype data for cereals.
• Select SNPDB»SEARCH to search genotype information stored in SNPDB.
• Search results can be downloaded in formats 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 SNPDB for future reference, to mark data that has to be deleted from SNPDB, or even as input for BINNER»SNP TAGS.
• For details on how to upload genotype data, please refer to the section on SNPDB»IMPORT.
• To browse the information available in SNPDB, please refer to the manual section on SNPDB»BROWSE.
• For details on how access to the data in SNPDB can be controlled, please refer to the manual sections on user groups.

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Search the SNPDB

• A SNPDB search involves three steps, illustrated on this screenshot of the SNPDB»SEARCH interface:
  1. Entering search parameters: In the top left-hand corner of the SNPDB»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, to delete data points or even to submit markers for binning).

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Entering search parameters

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

Please note: For each search, 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 further below.

• To launch a search, hit the SEARCH button.
• Searches are then listed in the "Search History" table on the top right-hand corner, where the number of "hits" for each search is shown 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.

Tag

This drop-down box gives you access to all the "SNPDB SAMPLE" and "SNPDB" tags 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) are listed.

File

Use the drop-down box to select data by the name of the imported file. Only files imported into the selected project(s) are listed.

Plate

Use the drop-down box to select data belonging to one or all of the plates. Only plates belonging to the selected file(s) are listed.

Species

Use the drop-down box to select the species of the samples used.

Marker

Use the drop-down box to select a listed marker to search for.

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) to stand for any number of characters (including zero characters); use "_" (the underscore symbol) to stand for exactly one character.
• If more than one SNPDB 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.

Genotype

Use the drop-down box to select a genotype to search for.

AR Range

Enter a minimum and maximum value for the allele ratio (AR) value in ASPE type SNP markers. Check the "Not in Range" box to search for those values NOT in the specified range.

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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 SNPDB»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 SNPDB 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" text box. 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 SNPDB 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.

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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, SNPDB entries are displayed on the lower half of the SNPDB»SEARCH interface.
• 'GENica Marker Tools' allows a choice of display options that can be further customised. SNPDB search results can be exported in their customised format.
• Search results can be tagged for downstream purposes.

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Change the way SNPDB search results are displayed and exported

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

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The SAMPLExMARKER view

• The "SamplexMarker view" displays marker names are arranged across the top of the table, sample names down the left-hand side.
• To prevent the creation of SamplexMarker tables 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 SamplexMarker table has more than 256 columns, please also refer to the section on spreadsheet viewers without a 256-column limitation.

• Use 'GENica Marker Tools' OPTIONS' to customise the SamplexMarker view:
  1. Choose whether to display the genotype or the AR value in the table.
  2. Select if the "ASPE Name" (e.g. "HvSNP.1a") or published marker names are displayed.

Please note: Search and display options are controlled separately, it is therefore possible e.g. to restrict a search by "ASPE Name" (see section on entering search parameters), but to display the search results with their "published" marker names.

• 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 SNPDB entries, switch to the "Table view" first.

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The TABLE view

• Switch to the "Table View" by selecting it from the drop-down box at the top right-hand side of the SNPDB search results table.
• All the SNPDB entries matching a query are listed. The information can extend over several results pagers. 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 by that column.
• Click on [SELECT COLUMNS] to open 'GENica Marker Tools' OPTIONS where the Table view can be customised:
  1. Select the columns to be displayed in the Table view by ticking / unticking the boxes under "SNPDB Table Fields". All the fields from the original SNPDB import file are available, plus extra fields created within 'GENica Marker Tools' (e.g. "User Group", "Project").
  2. Change the number of lines displayed on each page.
  3. Select if "ASPE Name" (e.g. "HvSNP.1a") or published marker names are displayed, if applicable.
• "Tag" search results for further use as described in the section on tagging.

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Export SNPDB 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-delimited *.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.

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TAG SNPDB 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 "SNPDB project" or "marker set", it now also forms part of a tag. This allows grouping entries from different projects, marker sets, user groups, plates, 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. Depending on the "type" of tag in question, choose TAGS»MARKERS, TAGS»SNPDB or TAGS»SNPDB SAMPLE.

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"SNPDB Tags" versus "SNPDB Sample Tags"

• When tagging SNPDB entries, select "SNPDB Sample Tags" to tag samples and "SNPDB Tags" to tag markers and the related allele values in a data set.
  • "SNPDB Sample Tags":
    • Tag SNPDB search results with a "SNPDB 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 SNPDB»SEARCH.
    • Tag SNPDB search results with a "SNPDB Sample Tag" to delete the selected samples from a SNPDB 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.
  • "SNPDB Tag":
    • Tag SNPDB search results with a "SNPDB Tag" to mark its markers for future reference. A SNPDB Tag can be opened within the MARKERS»SEARCH interface to access marker-specific information. A SNPDB Tag can be opened within the SNPDB»SEARCH interface to access which samples were genotyped with the tagged markers and what allele values were recorded.
    • Tag SNPDB search results with a "SNPDB Tag" to delete its markers from a SNPDB 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.
    • Tag SNPDB search results with a "SNPDB Tag" to bin the markers with BINNER»SNP TAGS, e.g. if errors noted in SNPDB require that genotyping is repeated in the lab for a couple of markers.

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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" ("SNPDB Tag" or "SNPDB Sample Tag") for the tag's purpose.
• Click SAVE to begin tagging. After tagging is complete, the TAGS»SNPDB or the TAGS»SNPDB SAMPLE interface opens, depending on the chosen tag type, where a tag can be reviewed, edited or deleted.

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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 SNPDB»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.

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Spreadsheet options for data arrays with more than 256 columns

• Arrays downloaded from GMT 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 only 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.

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Links to other user manual pages

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