<!DOCTYPE html SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\r
<!--\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\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
* \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
+<html xmlns="http://www.w3.org/1999/xhtml">\r
+<head>\r
+Database Reference Fetching\r
+</head>\r
+<p>\r
+<p><strong>Discovering Database References for Sequences</strong><br>\r
+Database references are associated with a sequence are displayed as a\r
+list in the tooltip shown when mousing over its sequence ID. Jalview\r
+uses references for the retrieval of <a\r
+ href="../features/viewingpdbs.html">PDB structures</a> and <a\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 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
+<p><strong>The Sequence Identification Process</strong><br>\r
+The method of accession id discovery is derived from the method which\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 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
+<p>If a record (or set of records) is retrieved by any query derived\r
+from the ID string of a sequence, then the sequence is aligned to the\r
+ones retrieved to determine the correct start and end residue positions\r
+(which are displayed when the 'Show Full Sequence ID' option). This is\r
+important for the correct display of the location of any features\r
+associated with that database.</p>\r
+<p>If the alignment reveals differences between the sequence in the\r
+alignment and the one in the record, then Jalview will assume that the\r
+aligned sequence is not the one in the retrieved record.</p>\r
+<p>In some cases, the ID used to retrieve records may be out\r
+of date and a dialog box will be opened indicating that a 100% match\r
+between the sequence and the record was identified, but the\r
+sequence name is different. In this case, the can be manually\r
+changed (by right clicking on the sequence ID and selecting <strong>Sequence→Edit\r
+Name</strong>).\r
+<ul>\r
+ <li><em>Note</em><br>\r
+ Please remember to save your alignment if either the start/end\r
+ numbering, or the sequence IDs were updated during the ID\r
+ retrieval process.</li>\r
+</ul>\r
+<body></body>\r
+</html>\r
git://source.jalview.org / jalview.git / blobdiff