News for Alpaca Ensembl Release 79 (March 2015)

News categories

New web displays and tools

Query hit distribution image on BLAST/BLAT results page

A new image view representing the distribution of the HSPs on your query sequence has been added to the BLAST/BLAT results page.

Display your BigWig files on whole chromosomes

We have updated our 'Whole genome' and 'Chromosome summary' pages to allow the display of BigWig data across a single chromosome or an entire karyotype. Simply attach your BigWig file through the 'Add your data' interface, then turn on the track in either view. Each wiggle point or histogram bar shows the mean value for that bin (where a bin is 150th of the length of the longest chromosome).

Note that the display across the entire genome will scale according to the maximum value in the entire file, whereas the chromosome display uses the maximum for that chromosome.

New species, assemblies and genebuilds

Vega Human annotation updated

Manual annotation of human from Havana has been updated and contains the data released in Vega 59

API and schema changes

Update to overlap/translation REST endpoint

Endpoint updated to provide only variations overlapping the protein sequence, not the whole transcript

Other updates

Compara

Regulation matrix tutorial

You can now close all the tutorial popup in the regulation matrix (in configuration panel) by clicking on the cross icon.

Schema version update

78 -> 79

Schema: support for polyploid genomes

There will be a new column "genome_component" in the genome_db table, with the appropriate API support

New SPECIES_TREE method

This will allow us to store species trees independently of datasets (needed for http://www.ensembl.org/info/about/speciestree.html)

API: remove GenomicAlignBlockAdaptor::fetch_all_by_MethodLinkSpeciesSet_GroupID()

The method is unused in the project, and there is no SQL index to speed it up.

Medaka vs Tetraodon lastz

Medaka vs Tetraodon lastz pairwise alignments (O.lat-T.nig lastz-net (on O.lat))

Medaka vs Tetraodon synteny

Medaka vs Tetraodon synteny

Web: statistics of the synteny analysis between two species

A new page similar to the statistics of the pairwise alignments, but over the synteny blocks. Since there is no specific alignmentsfor the synteny regions, the statistics only consist in covered / uncovered lengths.

Core

External database references update

Xrefs update for:

human, chicken, panda, sloth, armadillo, kangaroo rat, elephant, wallaby, pika, mouse lemur, rock hyrax, megabat, tasmanian devil, fugu, tarsier, dolphin, alpaca, xenopus

patch_78_79_b.sql - Support for BAMCOV

Schema support for future BAMCOV support in the web interface.

Stable ID lookup

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

Ensembl VM Build

The Ensembl Virtual Machine applicance will be updated to version 79.

LRG Import

Importing the latest version of Locus Reference Genomic dataset

patch_78_79_a.sql - schema_version update

Update schema_version in meta table to 79.

patch_78_79_a.sql - schema_version update in ontology db

Update schema_version in meta table to 79.

patch_78_79a.sql - schema_version update in production db

Update schema_version in production database to 79.

assembly.overlapping_regions retired

assembly.overlapping_regions meta_key retired and removed from core databases

marker.priority retired

marker.priority meta_key retired and removed from core databases

Support for polyploid genomes

New methods in the Slice object to provide support for polyploid genomes

Allows to fetch slices for a given component

Synonym types in ontologies

Ontology schema updated to provide the type for synonyms

Genebuild

All species: updated RefSeq gene import

RefSeq GFF3 annotation were added to the otherfeatures databases. Please note that RefSeq annotates gene models on cDNA sequence and not on the reference genome, meaning that when users choose to translate the RefSeq transcripts off the reference genome that the translations may contain stop codons.

Production

FASTA & GTF dumps

FASTA & GTF dumps for all the species

External reference projection

Gene ontology (GO) identifiers and gene name projection to all species.

Ensembl 79 mart databases

  • Ensembl Genes 79
    • Split up the id list and id list limit filters to separate external references from probes filters
      • Renamed "Limit to genes..." to "Limit to genes (external references)..." and "Limit to genes (microarray probes/probesets)..."

      • Renamed "ID list limit  [Max 500 advised]" to "Input external references ID list [Max 500 advised]" and "Input microarray probes/probesets ID list [Max 500 advised]"

    • Separated the Variation page into Variation (Germline) and Variation (Somatic)
      • Renamed "chromosome_location" internal name to "chromosome_start" and added a new attribute called "chromosome_end" in the Variation (Germline) page
      • Renamed "somatic_chromosome_location" internal name to "somatic_chromosome_start" and added a new attribute called "somatic_chromosome_end" in the Variation (Somatic) page
      • Renamed "Chromosome Location (bp)" attribute to "Chromosome position start (bp)" in both Variation (Germline) and Variation (Somatic) pages
    • Fruitfly (Drosophila melanogaster) assembly update from BDGP5 to BDGP6 and geneset update
    • Human assembly update from GRCh38 to GRCh38.p2
  • Ensembl Variation 79
    • Removed the "_20137" from all the variation_citation attributes internal names
    • Removed all the "_20126" from all the regulatory feature attributes internal names and prefixed all the internal names with "reg_"
    • Removed all the "_20125"  from all the motif feature attributes internal names and prefixed all the internal names with "motif_" 
    • Fruitfly (Drosophila melanogaster) assembly update from BDGP5 to BDGP6 and geneset update
    • Human assembly update from GRCh38 to GRCh38.p2
  • Ensembl Regulation 79
    • Brand new Regulation mart, faster, easier to use and packed with new features. Feature set has been split up into 6 sections.
    • Added Band Start and End filter
    • Added Marker Start and End filter
    • Added Encode region filter
    • Added SO name and accessions for the 6 Regulation sections
    • Added EFO Term accessions for Regulatory evidence, Regulatory features and Regulatory segments.
    • Added  "Has evidence" data to the Regulatory features section
    • Added Strand and "Evidence" to the miRNA Target Regions section.
  • Vega 59
    • Renamed "ID list limit  [Max 500 advised]" to "Input external references ID list [Max 500 advised]"

    • Human assembly update from GRCh38 to GRCh38.p2

EMBL and Genbank Dumps

EMBL and Genbank dumps for all species.

Web

New CAFE (gene gain/loss) tree View

We now have a new Gene gain/loss tree view.

http://www.ensembl.org/Homo_sapiens/Gene/SpeciesTree?g=ENSG00000174485;r=15:65658046-65792293

The new tree is faster and more interactive than the old tree.  You can also view the tree in a radial or vertical layout (click the double arrow icon on the image blue bar). And you can choose between minimal and full tree (click the tree icon on the image blue bar).

The following browsers support the new view:

IE 9 onwards;  Firefox 31 onwards; Chrome 31 onwards; Safari 5.1 onwards

For older browsers we will continue to show the previous version of the tree.

Moving away from EnsEMBL::Web::TmpFile

Our old file-handling modules in the EnsEMBL::Web::TmpFile namespace no longer supply all the functionality we need, so we are are in the process of moving to a new set of modules under EnsEMBL::Web::File. These new modules were already in use for the new export interface, but have been substantially expanded in release 79.

Web users should see no change in behaviour, but developers who have been using TmpFile should note that the old modules are now deprecated and will be removed within the next twelve months as we gradually port all file functionality to the new code.

"Download all tables" button has moved

In line with our other changes to the data export interface, the "Download view as CSV" button on pages with multiple tables has been moved to the main part of the page, above the first table, and renamed "Download all tables as CSV" for clarity.

Individual tables can still be downloaded separately using the Excel icon in the righthand corner of the blue header bar.

Retirement of archive 66

This release cycle we will be retiring archive 66 (Feb 2012) in accordance with our three-year rolling retirement policy. The data will remain available on our public database server; only the web interface will be removed.

Retirement of Sanger::Graphics modules

The following is only of relevance to developers who have created custom drawing code for their Ensembl-powered site:

As part of our "under the hood" maintenance of our codebase, we are planning to retire the Sanger::Graphics namespace and move all required functionality into EnsEMBL::Draw. The relevant modules and methods have been copied over, and the old ones will be removed in a future release.

Please note that if your code uses Sanger::Graphics::ColourMap, Bump or TextHelper, these modules have been moved into EnsEMBL::Draw::Utils.

Ensembl search in google search

There is now a search bar for www.ensembl.org when you get a hit to Ensembl in the results of a google search.

The code has been released but it might take a few days/weeks for google to pickup the changes and to show the search bar in google results.

TSL icon on transcript summary page

We are now showing the transcript support level (TSL) in the summary panel as an icon with a more detailed explanation available when you hover your mouse over it.

http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000128573;r=7:114414997-114693768;t=ENST00000403559

DAS Registry removal

Ensembl releases upto 78 have inspected the DAS Registry for DAS sources that can be attached to the browser. The Registry is being retired in May 2015 and consequently from Release 79 onwards Ensembl will no longer query the Registry. You might notice this as a decrease in the number of sources available via 'Manage Your Data' -> 'Attach DAS'

Removing feature counts on the left navigation

The feature counts in the left navigation (number in between bracket next to the links) has been removed on all the views and moved to the summary panel (top panel on the summary page).

A new line (About this gene, About this transcript, About this variant, About this structual variant) has been added on the gene summary, transcript summary, variation summary and structural variant summary page which lists the counts.

Share BLAST/BLAT/VEP results with others

Results from Ensembl tools can now be shared with others via URL. The feature is on by default i.e. the tickets can be shared to other by sharing the page's URL, but there is a checkbox in the Ticket List view that allows you to make your ticket non-sharable.

Downloading large VEP results

Downloading large VEP result text files is now possible.

View BLAST/BLAT results from multiple jobs on location view

Results from multiple BLAST/BLAT jobs can now be seen simultaneously on location views

Improved rendering of (Big)Bed features

Our drawing code has been updated to enable "intron-style" joins within alignment features, e.g. in BED files where these are defined using the blockCount/blockStart/blockSize columns. Select 'Structure' or 'Structure with labels' from the styles menu.

Colouring karyotype "pointers"

When viewing your own BED files on a karyotype, the drawing code now respects the itemRgb values for each feature, if set.

Popup userdata menus on karyotype

The karyotype has been updated with new popup menus for user data. Where features overlap on the genome, the popup menu will show an entry for every feature.