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<strong>Fetching ENSEMBL Data in Jalview</strong>
- <br /> Jalview Version 2.10 (September 2016) introduced support to
+ <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="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>
+ <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.<br />
+ <em>Ensembl support is new in Jalview, and we expect to merge
+ these sources in a future release.</em>
+ </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>
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