help/html/features/uniprotsequencefetcher.html

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  22 <head>
  23 <title>The Uniprot Free Text Search Interface</title>
  24 </head>
  25 <body>
  26
  27   <strong>The Uniprot Free Text Search Interface</strong>
  28   <p>
  29     Jalview provides a specialised interface that allows fast and
  30     efficient discovery and retrieval of data from the Uniprot database.
  31     It allows
  32     interactive querying of Uniprot metadata with free text and structured
  33     queries, so sequences can be located without prior knowledge of
  34     their database accessions, or <em>via</em> manual cross-referencing
  35     from Uniprot or other bioinformatics websites.
  36   </p>
  37   <p>
  38     To open the UniProt Sequence Fetcher, select UniProt as the database from
  39     any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em>
  40     <strong>&quot;File &#8594;Fetch Sequences&quot;</strong>).
  41   </p>
  42   <p>
  43   <img src="uniprotseqfetcher.png" align="left"
  44     alt="Uniprot sequence fetcher (introduced in Jalview 2.9.1)"
  45   />
  46   </p>
  47
  48   <p>
  49     <strong>Searching the Uniprot Database</strong>
  50   </p>
  51   <p>
  52     To search the Uniprot, begin typing in the text box. The results of your
  53     query are shown in the search results tab, which queries Uniprot after 1.5secs every time
  54     you type in the search text box. You can sort results according to
  55     the displayed columns, and select entries with the mouse or
  56     keyboard. Once you have selected one or more entries, hit the <strong>OK</strong>
  57     button to retrieve and visualise the sequences in Jalview Alignment interface.
  58   </p>
  59   <ul>
  60     <li><strong>Searching a specific Uniprot field </strong> If you
  61       want to find sequences based on a specific Uniprot metadata field,
  62       you can select it from the drop-down menu.</li>
  63
  64
  65                 <li><strong>Bulk Uniprot retrieval</strong><br>
  66       Firstly, switch the search target to Uniprot Id, then enter multiple IDs by separating them with a semi-colon.
  67       e.g. fila_human; mnt_human; mnt_mouse<br />Hitting Return or OK will automatically
  68       fetch those IDs, like the default Sequence Fetcher interface.</li>
  69
  70             <li><strong>Advanced / Custom querying</strong>
  71       The table below provides a brief overview of the supported Uniprot query syntax (see <a href="uniprotqueryfields.html">query fields for UniProtKB</a>):
  72                 <table border="1" width="95%">
  73                                 <tr>
  74                                         <td><code>human antigen</code></td>
  75                                         <td rowspan="3">All entries containing both terms.</td>
  76                                 </tr>
  77                                 <tr>
  78                                         <td><code>human AND antigen</code></td>
  79                                 </tr>
  80                                 <tr>
  81                                         <td><code>human &amp;&amp; antigen</code></td>
  82                                 </tr>
  83                                 <tr>
  84                                         <td><code>"human antigen"</code></td>
  85                                         <td>All entries containing both terms in the exact order.</td>
  86                                 </tr>
  87                                 <tr>
  88                                         <td><code>human -antigen</code></td>
  89                                         <td rowspan="3">All entries containing the term <code>human</code>
  90                                                 but not <code>antigen</code>.
  91                                         </td>
  92                                 </tr>
  93                                 <tr>
  94                                         <td><code>human NOT antigen</code></td>
  95                                 </tr>
  96                                 <tr>
  97                                         <td><code>human ! antigen</code></td>
  98                                 </tr>
  99                                 <tr>
 100                                         <td><code>human OR mouse</code></td>
 101                                         <td rowspan="2">All entries containing either term.</td>
 102                                 </tr>
 103                                 <tr>
 104                                         <td><code>human || mouse</code></td>
 105                                 </tr>
 106                                 <tr>
 107                                         <td><code>antigen AND (human OR mouse)</code></td>
 108                                         <td>Using parentheses to override boolean precedence rules.</td>
 109                                 </tr>
 110                                 <tr>
 111                                         <td><code>anti*</code></td>
 112                                         <td>All entries containing terms starting with <code>anti</code>.
 113                                                 Asterisks can also be used at the beginning and within terms. <strong>Note:</strong>
 114                                                 Terms starting with an asterisk or a single letter followed by an
 115                                                 asterisk can slow down queries considerably.
 116                                         </td>
 117                                 </tr>
 118                                 <tr>
 119                                         <td><code> author:Tiger*</code></td>
 120                                         <td>Citations that have an author whose name starts with <code>Tiger</code>.
 121                                                 To search in a specific field of a dataset, you must prefix your
 122                                                 search term with the field name and a colon. To discover what
 123                                                 fields can be queried explicitly, observe the query hints that are
 124                                                 shown after submitting a query or use the query builder (see
 125                                                 below).
 126                                         </td>
 127                                 </tr>
 128                                 <tr>
 129                                         <td><code>length:[100 TO *]</code></td>
 130                                         <td>All entries with a sequence of at least 100 amino acids.</td>
 131                                 </tr>
 132                                 <tr>
 133                                         <td><code>citation:(author:Arai author:Chung)</code></td>
 134                                         <td>All entries with a publication that was coauthored by two
 135                                                 specific authors.</td>
 136                                 </tr>
 137                         </table>
 138                 </li>
 139 </ul>
 140   <p>
 141     <strong>Result pagination</strong>
 142   </p>
 143   The query results returned from the Uniprot server are paginated for performance optimisation.
 144   The button labelled <strong>' << '</strong> and <strong>' >> '</strong> can be used to navigate to the next or previous result page respectively.
 145   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.
 146
 147
 148  <p>
 149     <strong>Customising The Uniprot Sequence Fetcher</strong>
 150   </p>
 151   <p>
 152     To change the displayed meta-data in the search result, click the
 153     'Customise Displayed Options' tab, and select the fields you'd like
 154     to displayed or remove.
 155   </p>
 156   <p>
 157     <em>The Uniprot Free Test Search Interface was introduced in
 158       Jalview 2.9.1</em>
 159   </p>
 160 </body>
 161 </html>