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-<head>
-<title>The UniProt Free Text Search Interface</title>
-</head>
-<body>
-
- <strong>The UniProt Free Text Search Interface</strong>
- <br /> Since version 2.10 (October 2016), the Jalview Desktop
- provides a search interface for interactive discovery and retrieval of
- sequence data from UniProt. This dialog enables UniProt sequence
- metadata to be searched with free text and structured queries, which
- allows sequences to be located via gene name, keywords, or even
- <em>via</em> manual cross-referencing from UniProt or other
- bioinformatics websites.
- <p>
- To open the UniProt Sequence Fetcher, select UniProt as the database
- from any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened
- <em>via</em> <strong>"File →Fetch
- Sequences"</strong>).
- </p>
- <p>
- <img src="uniprotseqfetcher.png" align="left"
- alt="UniProt sequence fetcher (introduced in Jalview 2.10)" />
- </p>
-
- <p>
- <a name="uniprotfts"><strong>Searching the UniProt Database</strong></a>
- </p>
- <p>To search UniProt, simply begin typing in the text box. If the
- 'autosearch' check box is enabled, then after a short delay (about
- 1.5 seconds), results will be shown in the table below. Results are
- also updated whenever you press Enter, and you can access previous
- searches by pressing the 'Down' arrow or clicking the drop-down menu
- icon at the side of the search box.</p>
- <p>You can sort results by clicking on the displayed columns,
- and select entries with the mouse or keyboard. Once you have
- selected one or more entries, hit the <strong>OK</strong> button to
- retrieve the sequences.
- </p>
- <ul>
- <li><strong>Searching a specific UniProt field </strong> To
- find sequences with particular UniProt metadata, you can select a
- field to search from the drop-down menu.</li>
-
-
- <li><strong>Bulk UniProt record retrieval</strong><br> To
- retrieve sequences for a list of Uniprot accessions, please enter
- them via the 'Retrieve IDs' tab.</li>
-
- <li><strong><a name="text-search">Complex queries
- with the UniProt query Syntax</a></strong> The text box also allows complex
- queries to be entered. The table below provides a brief overview
- of the supported syntax (see <a href="uniprotqueryfields.html">query
- fields for UniProtKB</a>):
- <table border="1" width="95%">
- <tr>
- <td><code>human antigen</code></td>
- <td rowspan="3">All entries containing both terms.</td>
- </tr>
- <tr>
- <td><code>human AND antigen</code></td>
- </tr>
- <tr>
- <td><code>human && antigen</code></td>
- </tr>
- <tr>
- <td><code>"human antigen"</code></td>
- <td>All entries containing both terms in the exact order.</td>
- </tr>
- <tr>
- <td><code>human -antigen</code></td>
- <td rowspan="3">All entries containing the term <code>human</code>
- but not <code>antigen</code>.
- </td>
- </tr>
- <tr>
- <td><code>human NOT antigen</code></td>
- </tr>
- <tr>
- <td><code>human ! antigen</code></td>
- </tr>
- <tr>
- <td><code>human OR mouse</code></td>
- <td rowspan="2">All entries containing either term.</td>
- </tr>
- <tr>
- <td><code>human || mouse</code></td>
- </tr>
- <tr>
- <td><code>antigen AND (human OR mouse)</code></td>
- <td>Using parentheses to override boolean precedence
- rules.</td>
- </tr>
- <tr>
- <td><code>anti*</code></td>
- <td>All entries containing terms starting with <code>anti</code>.
- Asterisks can also be used at the beginning and within
- terms. <strong>Note:</strong> Terms starting with an
- asterisk or a single letter followed by an asterisk can slow
- down queries considerably.
- </td>
- </tr>
- <tr>
- <td><code> author:Tiger*</code></td>
- <td>Citations that have an author whose name starts with
- <code>Tiger</code>. To search in a specific field of a
- dataset, you must prefix your search term with the field
- name and a colon. To discover what fields can be queried
- explicitly, observe the query hints that are shown after
- submitting a query or use the query builder (see below).
- </td>
- </tr>
- <tr>
- <td><code>length:[100 TO *]</code></td>
- <td>All entries with a sequence of at least 100 amino
- acids.</td>
- </tr>
- <tr>
- <td><code>citation:(author:Arai author:Chung)</code></td>
- <td>All entries with a publication that was coauthored by
- two specific authors.</td>
- </tr>
- </table></li>
- </ul>
- <p>
- <strong>Result pagination</strong>
- </p>
- The query results returned from the UniProt server are paginated for
- performance optimisation. The button labelled
- <strong>' << '</strong> and
- <strong>' >> '</strong> can be used to navigate to the
- next or previous result page respectively. The page range is shown on
- the title bar of the Free Text Search interface. Jalview's pagination
- implementation supports multiple selection of entries across multiple
- pages.
-
-
- <p>
- <strong>Customising The UniProt Sequence Fetcher</strong>
- </p>
- <p>To change the displayed meta-data in the search result, click
- the 'Customise Displayed Options' tab, and select the fields you'd
- like to be displayed or removed.</p>
- <p>
- <em>The UniProt Free Test Search Interface was introduced in
- Jalview 2.10.0</em>
- </p>
-</body>
-</html>
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