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New web displays and tools

New VEP interface (Saccharomyces cerevisiae)

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 (Saccharomyces cerevisiae)

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 (Saccharomyces cerevisiae)

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

Other updates

Saccharomyces cerevisiae (Saccharomyces cerevisiae)

Updated assembly name from EF4 to R64-1-1 to match the official INSDC name. Added lift over mappings

Saccharomyces cerevisiae - Otherfeatures (Saccharomyces cerevisiae)

Updated assembly name from EF4 to R64-1-1 to match the official INSDC name. Added lift over mappings

Ensembl 75 mart databases (Saccharomyces cerevisiae)

  • 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 (Saccharomyces cerevisiae)

EMBL and Genbank dumps for all species.

External reference projection (Saccharomyces cerevisiae)

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

FASTA & GTF dumps (Saccharomyces cerevisiae)

FASTA & GTF dumps for all the species

LRG Import (Saccharomyces cerevisiae)

Importing the latest version of Locus Reference Genomic dataset

Gene and Transcript Adaptor support for fetch_all_by_Source() (Saccharomyces cerevisiae)

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

SQLite Support (Saccharomyces cerevisiae)

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

input_subset.analysis_id (patch_74_75_c) (Saccharomyces cerevisiae)

An analysis_id has been added to the input_subset table, which will mirror the input_set.analysis_id. 

Consequently, InputSubset has been changed to inherit from Set, and the feature_type validation in of Set subclass constructors has been moved to the Set constructor.

This work is a prerequisite to the retiring the InputSet class/table.

InputSet retired (patch_74_75_d) (Saccharomyces cerevisiae)

The InputSet class has been retired and ResultSet will be used directly instead.  The result_set_input table has been patched to replace input_set entries with input_subset entries.  The ResultSet classes have been updated to make the association of dbfile_registry_entry record optional.

The InputSet class and table will remain in the schema, until all dependant code has been migrated to the new usage model.

Array size (Saccharomyces cerevisiae)

The Array size attribute and associated methods/constructor parameters have been deprecated or removed.

patch_74_75a.sql - schema_version update in production db (Saccharomyces cerevisiae)

Update schema_version in meta table to 75.

patch_74_75_c.sql (Saccharomyces cerevisiae)

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

Mircroarray mapping (Saccharomyces cerevisiae)

Microarray mapping has been updated for those species with new genome assemblies, new gene builds or new arrays.

patch_74_75_e.sql (Saccharomyces cerevisiae)

Attrib related tables do not allow duplicates

Unique key constraints added to enforce this

Experiment FeatureType and CellType (patch_74_75_f) (Saccharomyces cerevisiae)

The experiment table has had additional feature_type_id and cell_type_id fields added, and the associated API classes have been updated. This is in line with the current suage within the analysis pipelines and is to prevent the experiment class being used as a study where many feature/cell types can be associated.

ProteinTrees and homologies (Saccharomyces cerevisiae)

 

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 (Saccharomyces cerevisiae)

 

  • 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 (Saccharomyces cerevisiae)

 

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 (Saccharomyces cerevisiae)

 

  • [ ] 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 (Saccharomyces cerevisiae)

 

  •  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 (Saccharomyces cerevisiae)

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 (Saccharomyces cerevisiae)

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.

Remove read_coverage table (Saccharomyces cerevisiae)

The read_coverage table and associated API support will be removed.

There are only a few individuals across our resequencing data with read coverage data, much of which has been remapped between assemblies and may no longer be reliable.

Removing this will speed up code and clean up some of the web displays.

patch_74_75_a.sql - schema_version update in ontology db (Saccharomyces cerevisiae)

Update schema_version in meta table to 75.

patch_74_75b.sql - longer code in attrib_type (Saccharomyces cerevisiae)

'code' column in master_attrib_type table expanded

patch_74_75_f.sql - longer code (Saccharomyces cerevisiae)

'code' column in attrib_type table longer

Retirement of ensembl-draw (Saccharomyces cerevisiae)

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 (Saccharomyces cerevisiae)

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 (Saccharomyces cerevisiae)

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 (Saccharomyces cerevisiae)

Stable ID lookup provided for REST services

Removal of "default action" (Saccharomyces cerevisiae)

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 (Saccharomyces cerevisiae)

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 (Saccharomyces cerevisiae)

Update schema_version in meta table to 75.

patch_74_75_b.sql - transcript source (Saccharomyces cerevisiae)

Adding the source column to the transcript table

patch_74_75_d.sql - default source for transcripts (Saccharomyces cerevisiae)

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