From: Jim Procter Date: Fri, 16 Sep 2016 19:22:49 +0000 (+0100) Subject: JAL-2189 JAL-1705 JAL-1795 ensembl fetching docs X-Git-Tag: Release_2_10_0~20^2~41 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8a8fae1abd7a310cd22f5396ddd9283cea6fe053;p=jalview.git JAL-2189 JAL-1705 JAL-1795 ensembl fetching docs --- diff --git a/help/html/features/ensemblsequencefetcher.html b/help/html/features/ensemblsequencefetcher.html new file mode 100644 index 0000000..2a62caa --- /dev/null +++ b/help/html/features/ensemblsequencefetcher.html @@ -0,0 +1,56 @@ + + + +Fetching ENSEMBL Data in Jalview + + + + Fetching ENSEMBL Data in Jalview +
Jalview Version 2.10 (September 2016) introduced support to + retrieve annotated transcripts, peptides and genomic contigs from + ENSEMBL. +
+ 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). +

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