From d796e03de093e79af675ec649252ca6de1fb6aa1 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 3 Oct 2016 15:06:26 +0100 Subject: [PATCH] JAL-2189 ensembl sequence fetching, locus view and variant annotation transfer docs --- help/html/features/ensemblsequencefetcher.html | 86 ++++++++++++++++++------ 1 file changed, 65 insertions(+), 21 deletions(-) diff --git a/help/html/features/ensemblsequencefetcher.html b/help/html/features/ensemblsequencefetcher.html index 2a62caa..54b57a3 100644 --- a/help/html/features/ensemblsequencefetcher.html +++ b/help/html/features/ensemblsequencefetcher.html @@ -25,32 +25,76 @@ Fetching ENSEMBL Data in Jalview -
Jalview Version 2.10 (September 2016) introduced support to +
Jalview Version 2.10 (October 2016) introduced support to retrieve annotated transcripts, peptides and genomic contigs from ENSEMBL.
Database selection dialog for fetching sequences (introduced in Jalview 2.8)

Database selection dialog for fetching sequences (introduced in Jalview 2.8)

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.

General Use
If you have a set of Ensembl - peptide 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). -

+ 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.
+ Ensembl support is new in Jalview, and we expect to merge + these sources in a future release. +

+ 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. +

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