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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 (October 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="right" width="480" height="204"
- alt="Database selection dialog with Ensembl sequence source tooltip">
-
- <p>Two types of ENSEMBL source are provided. ENSEMBL queries the
- main ENSEMBL warehouse containing data for higher eukaryotes, and
- EnsemblGenomes, which queries Ensembl Pathogens, and other
- warehouses.</p>
- <p>
- <strong>General Use</strong><br /> If you have a set of Ensembl
- gene 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).<br />
- </p>
- <p>
- <strong><a name="ensemblannotation">Ensembl Sequence
- Features</a></strong><br /> Jalview 2.10 includes support for the
- visualisation and transfer genomic and transcriptomic sequence
- features onto protein product sequences. Retrieval of a genomic
- locus results in a set of transcripts that are annotated with
- nucleotide variant information and exonic regions. By default,
- intronic regions will be hidden.
- </p>
- <p>
- <strong><a name="variantvis">Variant information on
- Protein Products</a></strong><br />Jalview can translate genomic variant
- annotation into protein sequence variant codes for variants
- intersecting coding regions of a gene. To see this in action, use
- the <strong>Calculate→Show cross-references</strong> menu to
- view protein product sequences for the currently displayed (or
- selected) sequences. The same menu allows you to recover Ensembl
- exon, transcript and variant information when viewing UniProt
- sequences.
- </p>
- <p>
- <strong>Viewing more information about variant annotation</strong><br />
- Variants are highlighted as red sequence features on the protein
- sequence, with each one reporting all protein sequence variants
- observed at that position as a result of the genomic variants.
- Right-clicking a variant allows you to open the Ensembl Variants web
- page for each variant, via the <strong>Link</strong> submenu.
- </p>
- <p>
- <strong>Work in Progress !</strong><br />In the next few releases,
- we hope to improve and extend Jalview's support for working with
- Ensembl. If you have any problems, questions or suggestions then
- please get in contact with us via the Jalview discussion list.
- </p>
-</body>
-</html>
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