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New web displays and tools

New VEP interface (Spotted gar)

The VEP web interface has been completely overhauled and now offers:

  • new results page with summary charts, interactive filtering and more
  • more options and configuration
  • 750 variant limit removed - limits are now imposed only on uploaded file size
  • VEP now runs on a job submission system

Highlighting the current feature (Spotted gar)

In Region in detail and similar views, we currently highlight the feature you have come from so that it's easier to find amongst all the tracks. However if you would like to turn off this highlighting, e.g. in order to have a cleaner image to export, you can now do so via the control panel.

You'll find the option under 'Information and decorations', labelled 'Highlight current feature'.

New species, assemblies and genebuilds

Vega Zebrafish annotation updated (Spotted gar)

Manual annotation of zebrafish from Havana has been updated and contains the data released in Vega 55.

Other updates

Ensembl 75 mart databases (Spotted gar)

  • Ensembl Genes 75
    • Renamed Saccharomyces cerevisiae assembly from EF4 to R64-1-1
    • Added new Transcript source filter and attribute for all the species
    • Added new filter and attribute for VEGA protein ID and WormBase Gene Sequence-name accesssion.
    • Added new variation species turkey (Meleagris gallopavo)
    • Renamed "Protein domains" filter and attribute sections to "Protein domains and families".
  • Ensembl Variation 75
    • Added new variation species turkey (Meleagris gallopavo)
    • Renamed Saccharomyces cerevisiae assembly from EF4 to R64-1-1

EMBL and Genbank Dumps (Spotted gar)

EMBL and Genbank dumps for all species.

External reference projection (Spotted gar)

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

FASTA & GTF dumps (Spotted gar)

FASTA & GTF dumps for all the species

LRG Import (Spotted gar)

Importing the latest version of Locus Reference Genomic dataset

Gene and Transcript Adaptor support for fetch_all_by_Source() (Spotted gar)

GeneAdaptor and TranscriptAdaptor will support the retrieval of their respective feature objects by the new source column

SQLite Support (Spotted gar)

The Ensembl core API will support SQLite databases. This work has been contributed by the Anacode team at the WTSI.

patch_74_75a.sql - schema_version update in production db (Spotted gar)

Update schema_version in meta table to 75.

patch_74_75_c.sql (Spotted gar)

Adding a new table genome_statistics

Populated during the production run, it contains basic statistics on the number of genes, the length of the genome or the number of prediction

patch_74_75_e.sql (Spotted gar)

Attrib related tables do not allow duplicates

Unique key constraints added to enforce this

ProteinTrees and homologies (Spotted gar)

 

GeneTrees (protein-coding) with new/updated genebuilds and assemblies

  • all-vs-all blastp (ncbi-blast-2.2.28+)
  • Clustering using hcluster_sg
  • Multiple sequence alignments using MCoffee (Version_9.03.r1318) or Mafft (mafft-7.113)
  • Phylogenetic reconstruction using TreeBeST
  • Homology inference
  • Pairwise gene-based dN/dS scores for high coverage species pairs only (both on orthologues and paralogues) (codeml/PAML v4.3)
  • GeneTree stable ID mapping
  • Per family gene dynamics using CAFE (v2.2)

ncRNAtrees and homologies (Spotted gar)

 

  • Classification based on Rfam models (v11.0)
  • Multiple sequence alignments with Infernal
  • Phylogenetic reconstruction using RAxML
  • Phylogenetic reconstruction using FastTree2 and RAxML-Light for very big families
  • Additional multiple sequence alignments with Prank (w/ genomic flanks)
  • Additional phylogenetic reconstruction using PhyML and NJ
  • Phylogenetic tree merging using TreeBeST
  • Per family gene dynamics using CAFE
  • Homology inference
  • Secondary structure plots

Protein Families (Spotted gar)

 

Updated MCL families including all Ensembl transcript isoforms (including human non-reference haplotypes) and newest Uniprot Metazoa.

  • Getting distances by NCBI BlastP (v.2.2.28+)
  • Clustering by MCL (v.12-135)
  • Multiple Sequence Alignments with MAFFT (v.7.113)
  • Family stable ID mapping

Compara dumps (Spotted gar)

 

  • [ ] Data dumps for ProteinTrees
  • [ ] Data dumps for ncRNAtrees
  • [ ] OrthoXML dumps for ProteinTrees
  • [ ] OrthoXML dumps for ncRNAtrees
  • [ ] PhyloXML dumps for ProteinTrees
  • [ ] PhyloXML dumps for ncRNAtrees

API/schema changes (Spotted gar)

 

  •  Extend genome_db table (and the corresponding API) with two extra fields (has_karyotype and is_high_coverage)
  •  Annotation of web display information in species_tree_node's instead of species_set_tags

Link from Region in Detail to individual exons (Spotted gar)

The popup menu that appears when you click on a transcript now includes a link to the Exon table if you click on an individual exon, and the exon you clicked on is shown in bold on the table. Note that this link will only appear when you are zoomed in enough for the click coordinates to clearly identify a single exon.

Retirement of archive 61 (Spotted gar)

This release cycle we will be retiring archive 61 (Feb 2011), 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.

patch_74_75_a.sql - schema_version update in ontology db (Spotted gar)

Update schema_version in meta table to 75.

patch_74_75b.sql - longer code in attrib_type (Spotted gar)

'code' column in master_attrib_type table expanded

patch_74_75_f.sql - longer code (Spotted gar)

'code' column in attrib_type table longer

Retirement of ensembl-draw (Spotted gar)

The ensembl-draw repository has been merged with ensembl-webcode.

The files that were in ensembl-draw can now be found in ensembl-webcode/modules/Sanger/Graphics and ensembl-webcode/modules/Bio/EnsEMBL.

Documentation move (Spotted gar)

To aid internal management of git permissions, we will be moving ensembl-webcode/htdocs/info into a separate public plugin, docs. No page URLs will change, but external developers will need to enable this plugin in order to display documentation for the API, etc on an Ensembl-powered website.

ensembl-webcode directory (Spotted gar)

Web code is now stored inside the top level directory ensembl-webcode.

A new variable has been added to SiteDefs, called $ENSEMBL_WEBROOT, which has the value of "$ENSEMBL_SERVERROOT/ensembl-webcode", and is used when locating files and directories that are inside ensembl-webcode. $ENSEMBL_SERVERROOT remains unchanged.

Stable ID lookup (Spotted gar)

Stable ID lookup provided for REST services

Removal of "default action" (Spotted gar)

We have removed the web behaviour whereby invalid URLs for genomic views were silently redirected to the default view for that gene/location/etc. This was causing issues with some scripts connecting to the website, including our own selenium testing. Invalid URLs now show a custom 404 component within the standard page template.

Search enhancments (Spotted gar)

Ensembl search has a number of improvements including (i) more extensive highlighting of the search term on the results page, (ii) improved ordering of results, and (iii) better handling of non alphanumeric characters in search queries.

patch_74_75_a.sql - schema_version update (Spotted gar)

Update schema_version in meta table to 75.

patch_74_75_b.sql - transcript source (Spotted gar)

Adding the source column to the transcript table

patch_74_75_d.sql - default source for transcripts (Spotted gar)

The new Transcript source column required a default value, that is now set to ensembl.