<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\r
+<!--\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+-->\r
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<head>\r
Database Reference Fetching\r
href="../features/dasfeatures.html">DAS features</a>, and for\r
retrieving sequence cross-references such as the protein products of a\r
DNA sequence.</p>\r
+<p><strong>Initiating reference retrieval</strong><br>\r
+The application provides three ways to access the retrieval function. Either:\r
+<ul><li>select the <strong>Discover PDB IDs</strong> option from the structure submenu of the sequence's popup menu</li>\r
+<li>Choose one of the options from the 'Fetch DB Refs' submenu in the alignment window's <strong>Web Services</strong> menu:<ul>\r
+<li><em>Standard Databases</em> will fetch references from the EBI databases plus currently selected DAS sources</li>\r
+<li>The other entries submenus leading to lists of individual database sources that Jalview can access.</li></ul></li>\r
+<li>Answer 'Yes' when asked if you wish to retrieve database references for your sequences after initiating a DAS Sequence Feature fetch.</li>\r
+</ul> \r
<p>Jalview discovers references for a sequence by generating a set\r
of ID queries from the ID string of each sequence in the alignment. It\r
-then tries to query all the databases it can access in order to match\r
+then tries to query a subset of all the databases it can access in order to match\r
the alignment sequence to any records retrieved from the database. If a\r
match is found, then the sequence is annotated with that database's\r
reference, and any cross-references that it's records contain.</p>\r
earlier Jalview versions used for Uniprot sequence feature retrieval,\r
and was originally restricted to the identifaction of valid Uniprot\r
accessions.<br>\r
-Essentially, Jalview will try to retrieve records from all the databases\r
+Essentially, Jalview will try to retrieve records from a subset of the databases\r
accessible by the <a href="../features/seqfetch.html">sequence\r
fetcher</a> using each sequence's ID string (or each string in the ID\r
separated by the '∣' symbol).</p>\r
retrieval process.</li>\r
</ul>\r
<body></body>\r
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+</html>\r
git://source.jalview.org / jalview.git / blobdiff