X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fseqfetch.html;h=8c4e462313e7b74c5c3446fedcfd9916eb1fdc2a;hb=refs%2Fheads%2Fmerge%2FJAL-1988_JAL-3772%2BJAL-3416%2BJAL-4054%2BJAL-4064;hp=e726c495607fd6176f4a8e0d6a7cf699ea02d450;hpb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;p=jalview.git

diff --git a/help/help/html/features/seqfetch.html b/help/help/html/features/seqfetch.html
index e726c49..8c4e462 100755
--- a/help/help/html/features/seqfetch.html
+++ b/help/help/html/features/seqfetch.html
@@ -38,7 +38,7 @@
       the database you want to retrieve sequences</strong> from the database
     chooser.
   </p>
-  <img src="selectfetchdb.gif" align="left" width="480" height="204"
+  <img src="selectfetchdb.gif" align="left"
     alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
   <p>
     The databases are shown as a tree, and ordered alphabetically;
@@ -69,17 +69,43 @@
         accession ids</strong> (as a semi-colon separated list), or press the
       &quot;Example&quot; button to paste the example accession for the
       currently selected database into the retrieval box. Finally, press
-      &quot;OK&quot; to initiate the retrieval.</li>
+      &quot;OK&quot; to initiate the retrieval.
+      <br />
+      For the PDB and UniProt sequence fetchers, choose the "Retrieve IDs" tab
+      to search for accession ids.</li>
   </ol>
 
-  <p>If you use the WSDBFetch sequence fetcher services (EMBL,
-    UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
-  <p>
-    Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
-    J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
-    R. <br> SOAP-based services provided by the European
-    Bioinformatics Institute.<br> Nucleic Acids Res. 33(1):W25-W28
-    (2005) <br> <br>
-  </p>
+  <p>If you use the Sequence Fetcher, please remember to cite the
+    corresponding services (linked to below):</p>
+  <ul>
+    <li>Ensembl - <a
+      href="https://github.com/Ensembl/ensembl-rest/wiki#citing">The
+        Ensembl REST API</a></li>
+    <li>EMBL/EMBLCDS - Provided by the <a
+      href="https://www.ebi.ac.uk/ena/browser/api/#/ENA_Browser_Data_API/getFlatFileUsingGET">European
+        Nucleotide Archive's ENA Data API</a><br />
+    <em>Note: Versions of Jalview prior to 2.11.1.1 employed the
+        XML endpoint of the ENA browser, which was retired in August
+        2020.</em></li>
+    <li>Uniprot - Free Text Search and Retrieval via the <a
+      href="https://www.uniprot.org/help/api">Uniprot REST API</a></li>
+    <li>PDB - Free Text Search via the <a
+      href="https://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
+        REST API</a> and retrieval via <a
+      href="https://www.ebi.ac.uk/Tools/dbfetch/">WSDbFetch</a><br />
+      Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
+      J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
+      R. <br> SOAP-based services provided by the European
+      Bioinformatics Institute.<br> Nucleic Acids Res.
+      33(1):W25-W28 (2005) <br> <br>
+    </li>
+    <li>
+      <a href="https://docs.rfam.org/en/latest/citing-rfam.html#rfam-references">RFAM - a database of RNA families</a>
+    </li>
+    <li>
+      <a href="https://pfam-docs.readthedocs.io/en/latest/citing-pfam.html">PFAM - a database of protein families</a><br/>
+      <a href="https://academic.oup.com/nar/article/49/D1/D344/5958491">Data is provided by the Interpro Web API</a>
+    </li>
+  </ul>
 </body>
 </html>