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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
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+ * Jalview is distributed in the hope that it will be useful, but
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>The Uniprot Free Text Search Interface</title>
+</head>
+<body>
+
+ <strong>The Uniprot Free Text Search Interface</strong>
+ <p>
+ Jalview provides a specialised interface that allows fast and
+ efficient discovery and retrieval of data from the Uniprot database.
+ It allows
+ interactive querying of Uniprot metadata with free text and structured
+ queries, so sequences can be located without prior knowledge of
+ their database accessions, or <em>via</em> manual cross-referencing
+ from Uniprot or other bioinformatics websites.
+ </p>
+ <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 2.9.1)"
+ />
+ </p>
+
+ <p>
+ <strong>Searching the Uniprot Database</strong>
+ </p>
+ <p>
+ To search the Uniprot, begin typing in the text box. The results of your
+ query are shown in the search results tab, which queries Uniprot after 1.5secs every time
+ you type in the search text box. You can sort results according to
+ 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 and visualise the sequences in Jalview Alignment interface.
+ </p>
+ <ul>
+ <li><strong>Searching a specific Uniprot field </strong> If you
+ want to find sequences based on a specific Uniprot metadata field,
+ you can select it from the drop-down menu.</li>
+
+
+ <li><strong>Bulk Uniprot retrieval</strong><br>
+ Firstly, switch the search target to Uniprot Id, then enter multiple IDs by separating them with a semi-colon.
+ e.g. fila_human; mnt_human; mnt_mouse<br />Hitting Return or OK will automatically
+ fetch those IDs, like the default Sequence Fetcher interface.</li>
+
+ <li><strong>Advanced / Custom querying</strong>
+ The table below provides a brief overview of the supported Uniprot query 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 displayed or remove.
+ </p>
+ <p>
+ <em>The Uniprot Free Test Search Interface was introduced in
+ Jalview 2.9.1</em>
+ </p>
+</body>
+</html>
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