2.06

[jalview.git] / help / html / features / seqfeatures.html

diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html
index 4026071..6264724 100755 (executable)
--- a/help/html/features/seqfeatures.html
+++ b/help/html/features/seqfeatures.html
@@ -8,36 +8,51 @@
 <p>Currently, sequence features are rendered in red or blue, dependent\r
   upon their type:</p><ul>\r
   <li>Features associated with a particular residue are coloured\r
-  red<br><italic>e.g. an active site residue</italic></li>\r
+  red<br><em>e.g. an active site residue</em></li>\r
   <li>Features which span a region are coloured blue<br>\r
-<italic>e.g. a region of sequence with known structure</italic></p>\r
-<p>More information about the feature is given in a tooltip, which are\r
+<em>e.g. a region of sequence with known structure</em>\r
+</li>\r
+</ul></p>\r
+<p>More information about the feature is given in a tooltip, which is\r
   viewed by moving the mouse pointer over a sequence feature. The\r
-  associated text for the feature will then be displayed in a small\r
-  label will appear near the pointer.</p>\r
+  description associated with the feature will then be displayed in a small\r
+  label near the pointer.</p>\r
 <p>After the Sequence Features option is selected, there may be some delay before\r
-  the features are actually rendered, as jalview must first determine if a\r
-  sequence is contained in uniprot and then retrieve its sequence\r
-  record. This delay should only happen once for a particular\r
-  alignment, as jalview caches uniprot records in a file in your home\r
+  the features are actually rendered, as jalview first determines if\r
+  the sequences are contained in Uniprot and then retrieves any sequence\r
+  records. This delay will normally only happen once for a particular\r
+  set of sequences, as jalview caches uniprot records in a file in your home\r
   directory called '.jalview.uniprot.xml'.\r
 \r
-<p>The first step in this process is to try to use the ID (name) of\r
-  each sequence as an ID search in Uniprot. If there is no match, The\r
-  EBI Blast search is used in an attempt to obtain the Uniprot Id for\r
-  each sequence. You will be  notified of any 100% matches with\r
-  Uniprot, but you must then manually change the name of the sequence,\r
-  by right clicking on the sequence ID and selecting\r
-  Sequence&#8594;Edit Name, before Jalview will show its sequence\r
+  <p><strong>The Sequence Identification Process</strong>\r
+\r
+  </p>\r
+<p>The first step in the procedure for matching uniprot IDs to\r
+  sequences is to use the ID (name) of\r
+  each sequence to retrieve Uniprot records directly.</p>\r
+<p>\r
+  If a uniprot record (or set of records) is found for a sequence,\r
+  then the sequence is aligned to the one in the Uniprot record\r
+  to determine the correct start and end residue positions (which are\r
+  displayed when the 'Show Full Sequence ID' option is set).\r
+</p>\r
+\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\r
+  the aligned sequence is not the one in the uniprot record.\r
+\r
+  </p>\r
+\r
+  <p> \r
+  In some cases, the ID used to retrieve Uniprot records may be out of\r
+  date and you will be notified of that a 100% match between the\r
+  sequence and a Uniprot record was identified, but the sequence name\r
+  must be manually changed (by right clicking on the sequence ID and selecting\r
+  <strong>Sequence&#8594;Edit Name</strong>), before Jalview will show its sequence\r
   features.<ul>\r
   <li>remember to save your alignment if you have updated any of the\r
   sequence IDs!\r
   </li>\r
   </ul></p>\r
-<p>\r
-  If a uniprot record (or set of records) is found for a sequence,\r
-  then the sequence in aligned to the one in the Uniprot record\r
-  to determine the correct start and end residue positions that will be\r
-  displayed when the 'Show Full Sequence ID' option is set.</p>\r
 </body>\r
 </html>\r