--- /dev/null
+<html>
+<!--
+ * 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.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * 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>
+ <br /> Since version 2.10 (September 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>
+ <strong>Searching the UniProt Database</strong>
+ </p>
+ <p>
+ To search UniProt, simply begin typing in the text box. After a
+ short delay (uabout 1.5 seconds), results will be shown in the table
+ below. 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 several uniprot accessions at once, first select <strong>UniProt
+ ID</strong> from the dropdown menu, then paste in the accession IDs as a
+ semi-colon separated list. (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><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 displayed or remove.</p>
+ <p>
+ <em>The UniProt Free Test Search Interface was introduced in
+ Jalview 2.10.0</em>
+ </p>
+</body>
+</html>
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff