X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fseqfeatures.html;h=6264724ce52839f3b42f6abb9865df9a744ec475;hb=14e8b69c8c3c474d77dbdf317565bbf37094185a;hp=88a4d5d4fe4c4c60c7a2fc546f9f6b7e5b1675a1;hpb=baf23db52aa82cca72d088c0c850b01562599c67;p=jalview.git

diff --git a/help/html/features/seqfeatures.html b/help/html/features/seqfeatures.html
index 88a4d5d..6264724 100755
--- a/help/html/features/seqfeatures.html
+++ b/help/html/features/seqfeatures.html
@@ -13,33 +13,46 @@
 <em>e.g. a region of sequence with known structure</em>
 </li>
 </ul></p>
-<p>More information about the feature is given in a tooltip, which are
+<p>More information about the feature is given in a tooltip, which is
   viewed by moving the mouse pointer over a sequence feature. The
-  associated text for the feature will then be displayed in a small
-  label will appear near the pointer.</p>
+  description associated with the feature will then be displayed in a small
+  label near the pointer.</p>
 <p>After the Sequence Features option is selected, there may be some delay before
-  the features are actually rendered, as jalview must first determine if a
-  sequence is contained in uniprot and then retrieve its sequence
-  record. This delay should only happen once for a particular
-  alignment, as jalview caches uniprot records in a file in your home
+  the features are actually rendered, as jalview first determines if
+  the sequences are contained in Uniprot and then retrieves any sequence
+  records. This delay will normally only happen once for a particular
+  set of sequences, as jalview caches uniprot records in a file in your home
   directory called '.jalview.uniprot.xml'.
 
-<p>The first step in this process is to try to use the ID (name) of
-  each sequence as an ID search in Uniprot. If there is no match, The
-  EBI Blast search is used in an attempt to obtain the Uniprot Id for
-  each sequence. You will be  notified of any 100% matches with
-  Uniprot, but you must then manually change the name of the sequence,
-  by right clicking on the sequence ID and selecting
-  Sequence&#8594;Edit Name, before Jalview will show its sequence
+  <p><strong>The Sequence Identification Process</strong>
+
+  </p>
+<p>The first step in the procedure for matching uniprot IDs to
+  sequences is to use the ID (name) of
+  each sequence to retrieve Uniprot records directly.</p>
+<p>
+  If a uniprot record (or set of records) is found for a sequence,
+  then the sequence is aligned to the one in the Uniprot record
+  to determine the correct start and end residue positions (which are
+  displayed when the 'Show Full Sequence ID' option is set).
+</p>
+
+<p>If the alignment reveals differences between the sequence in the
+  alignment and the one in the record, then Jalview will assume that
+  the aligned sequence is not the one in the uniprot record.
+
+  </p>
+
+  <p> 
+  In some cases, the ID used to retrieve Uniprot records may be out of
+  date and you will be notified of that a 100% match between the
+  sequence and a Uniprot record was identified, but the sequence name
+  must be manually changed (by right clicking on the sequence ID and selecting
+  <strong>Sequence&#8594;Edit Name</strong>), before Jalview will show its sequence
   features.<ul>
   <li>remember to save your alignment if you have updated any of the
   sequence IDs!
   </li>
   </ul></p>
-<p>
-  If a uniprot record (or set of records) is found for a sequence,
-  then the sequence in aligned to the one in the Uniprot record
-  to determine the correct start and end residue positions that will be
-  displayed when the 'Show Full Sequence ID' option is set.</p>
 </body>
 </html>