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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 (October 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)">
36 Two types of ENSEMBL source are provided. ENSEMBL queries the main
37 ENSEMBL warehouse containing data for higher eukaryotes, and
38 EnsemblGenomes, which queries Ensembl Pathogens, and other
39 warehouses.<br /> <em>Ensembl support is new in Jalview, and
40 we expect to merge these sources in a future release.</em>
43 <strong>General Use</strong><br /> If you have a set of Ensembl
44 gene or transcript IDs, then you can retrieve them <em>via</em> the
45 sequence fetcher dialog opened after selecting the most appropriate
46 source (either 'ENSEMBL', or Ensembl Genomes). However, Jalview's
47 Ensembl client has a couple of additional capabilities:
50 <strong>Retrieving aligned transcripts for a genomic ID</strong>
52 <p>If a single genomic identifier is entered in the Ensembl
53 fetcher, Jalview will return all transcripts and products for the
54 locus, and display them in a split view - complete with sequence
55 variant annotation.</p>
57 <strong>Retrieving orthologs for a gene ID</strong>
60 If a gene ID is entered (e.g. fox1), Jalview will resolve Ensembl
61 genomic identifiers for a predefined set of taxa (Mouse, Rat, Human,
62 Yeast in Jalview 2.10).<br />
65 <strong><a name="ensemblannotation">Ensembl Sequence
66 Features</a></strong><br /> Jalview 2.10 includes support for the
67 visualisation and transfer genomic and transcriptomic sequence
68 features onto protein product sequences. Retrieval of a genomic
69 locus results in a set of transcripts that are annotated with
70 nucleotide variant information and exonic regions. By default,
71 intronic regions will be hidden.
74 <strong><a name="variantvis">Variant information on
75 Protein Products</a></strong><br />Jalview can translate genomic variant
76 annotation into protein sequence variant codes for variants
77 intersecting coding regions of a gene. To see this in action, use
78 the <strong>Calculate→Show cross-references</strong> menu to
79 view protein product sequences for the currently displayed (or
80 selected) sequences. The same menu allows you to recover Ensembl
81 exon, transcript and variant information when viewing UniProt
85 <strong>Viewing more information about variant annotation</strong><br />
86 Variants are highlighted as red sequence features on the protein
87 sequence, with each one reporting all protein sequence variants
88 observed at that position as a result of the genomic variants.
89 Right-clicking a variant allows you to open the Ensembl Variants web
90 page for each variant, via the <strong>Link</strong> submenu.
93 <strong>Work in Progress !</strong><br />In the next few releases,
94 we hope to improve and extend Jalview's support for working with
95 Ensembl. If you have any problems, questions or suggestions then
96 please get in contact with us via the Jalview discussion list.