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;
accession ids</strong> (as a semi-colon separated list), or press the
"Example" button to paste the example accession for the
currently selected database into the retrieval box. Finally, press
- "OK" to initiate the retrieval.</li>
+ "OK" 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>