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23 <title>Fetching ENSEMBL Data in Jalview</title>
27 <strong>Fetching ENSEMBL Data in Jalview</strong>
28 <br /> Jalview Version 2.10 (September 2016) introduced support to
29 retrieve annotated transcripts, peptides and genomic contigs from
30 <a href="http://www.ensembl.org">ENSEMBL</a>.
32 <img src="selectfetchdb.gif" align="left" width="480" height="204"
33 alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
35 <p>Two types of ENSEMBL source are provided. ENSEMBL queries the
36 main ENSEMBL site, which only serves data for higher eukaryotes, and
37 EnsemblGenomes, which provides access to Ensembl Pathogens, and
39 <p><strong>General Use</strong><br/> If you have a set of Ensembl
40 peptide or transcript IDs, then you can retrieve them
41 <em>via</em> the sequence fetcher dialog opened after selecting the
42 most appropriate source (either 'ENSEMBL', or Ensembl Genomes).
43 However, Jalview's Ensembl client has a couple of additional
44 capabilities: </p><p><strong>Retrieving aligned transcripts for a genomic ID</strong>
46 <p>If a single genomic identifier is entered in the
47 Ensembl fetcher, Jalview will return all transcripts and products
48 for the locus, and display them in a split view - complete with
49 sequence variant annotation.</p>
50 <p><strong>Retrieving orthologs for a gene ID</strong></p>
51 <p>If a gene ID is entered (e.g. fox1), Jalview will resolve
52 Ensembl genomic identifiers for a predefined set of taxa (Mouse,
53 Rat, Human, Yeast in Jalview 2.10).