-
- 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.
-
- General Use
If you have a set of Ensembl
- gene or transcript IDs, then you can retrieve them via 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:
-
- Retrieving aligned transcripts for a genomic ID -
-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.
-- Retrieving orthologs for a gene ID -
-
- 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).
-
- Ensembl Sequence
- Features
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.
-
- Variant information on
- Protein Products
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 Calculate→Show cross-references 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.
-
- Viewing more information about variant annotation
- 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 Link submenu.
-
- Work in Progress !
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.
-