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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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+<head>
+<title>Fetching ENSEMBL Data in Jalview</title>
+</head>
+<body>
+
+ <strong>Fetching ENSEMBL Data in Jalview</strong>
+ <br /> Jalview Version 2.10 (September 2016) introduced support to
+ retrieve annotated transcripts, peptides and genomic contigs from
+ <a href="http://www.ensembl.org">ENSEMBL</a>.
+ <br />
+ <img src="selectfetchdb.gif" align="left" width="480" height="204"
+ alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
+
+ <p>Two types of ENSEMBL source are provided. ENSEMBL queries the
+ main ENSEMBL site, which only serves data for higher eukaryotes, and
+ EnsemblGenomes, which provides access to Ensembl Pathogens, and
+ other warehouses.</p>
+ <p><strong>General Use</strong><br/> If you have a set of Ensembl
+ peptide or transcript IDs, then you can retrieve them
+ <em>via</em> the sequence fetcher dialog opened after selecting the
+ most appropriate source (either 'ENSEMBL', or Ensembl Genomes).
+ However, Jalview's Ensembl client has a couple of additional
+ capabilities: </p><p><strong>Retrieving aligned transcripts for a genomic ID</strong>
+ </p>
+ <p>If a single genomic identifier is entered in the
+ Ensembl fetcher, Jalview will return all transcripts and products
+ for the locus, and display them in a split view - complete with
+ sequence variant annotation.</p>
+ <p><strong>Retrieving orthologs for a gene ID</strong></p>
+ <p>If a gene ID is entered (e.g. fox1), Jalview will resolve
+ Ensembl genomic identifiers for a predefined set of taxa (Mouse,
+ Rat, Human, Yeast in Jalview 2.10).
+ </p>
+</body>
+</html>
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