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Ensembl News for Release 76 (August 2014)

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New web displays and tools

New BLAST interface (all species)

Ensembl are delighted to announce the release of our new BLAST/BLAT interface, which uses the same Tools infrastructure as the new web-based VEP that came out in release 75.

Highlights include:

  • Tickets saved to a user-friendly table so you can come back later and view or re-run your search
  • Automatic polling of the backend process - no more clicking "Retrieve"!
  • Better error-reporting, so that you can find out more easily why a job failed
  • We now use ncbi-blast instead of wu-blast - this gets around the licensing issues associated with the latter and enables us to distribute our blast code more freely

Please let us know what you think!

Datahub listings (all species)

Ensembl has had support for datahubs (also known as track hubs) for some time, and we have now added a page listing available public hubs for our species. Where appropriate, a link will take you to the sample location for a species and open the control panel so that you can easily configure the hub.

Please note that, particularly with the recent release of human GRCh38, many of these hubs are on old assemblies, so where possible* our links will take you to the most recent archive which included that assembly.

If you have a datahub that you would like including in our registry, please contact us.

* Some assemblies are only available on archives that predate datahub support

Regulation displays (Human)

The display of regulatory regions has been updated to coincide with the release of the data from the new Regulatory build. The major enhancement is a redesigned interface for selecting which types of evidence to display and for which cell types. In addition it allows for easier configuration of how to display that evidence, for example as peaks or as signals.

New Assembly Converter interface (all species)

In addition to the new BLAST interface, we have updated our online Assembly Converter to help our users migrate to GRCh38. The new tool currently uses CrossMap, which means input is limited to the following formats:

  • BED
  • GFF
  • GTF
  • VCF
  • WIG

For more information, see our online documentation on file format specifications.

(CrossMap also supports BigBED and BigWIG, but we are unable to offer upload of large files at the moment. We recommend using CrossMap locally if you have very large datasets to process.)

Initially we are offering this tool only for human assembly mappings GRCh37 -> GRCh38 and NCBI36 -> GRCh38. More species will be added as soon as we have the chain files available.

Important note: CrossMap discards file metadata such as track lines. We are working to implement an updated assembly mapper that preserves metadata, which will be released in a future version of Ensembl.

New page - news by topic (all species)

In addition to viewing all news for a given release, you can now view all news on a given topic, sorted in reverse chronological order. For example if you want to see all new web features for the last several releases, you can use this link (which also appears on the home page):

All web updates, by release

The following topics are also available:

We hope you find this page useful!

New interface for sequence export (all species)

We are embarking on an upgrade of our Export interface, to make it simpler to use and more directly related to the data you see on screen. The first component to be released is for "text sequence" pages, i.e. views that show DNA or peptide sequence as text.

Features of the new interface:

  • Single interface for FASTA and RTF output
  • Improved support for RTF fonts and background colours in OSX
  • Select "uncompressed" or "gzipped" in the same input form as your other output options, rather than having to click on a second link
  • Uncompressed output can be copied'n'pasted from the file preview or downloaded onto your computer

Note that we have removed the old "HTML" format for FASTA as it was irrelevant in the new interface.

[screenshot]

Also, the old "Export data" button has been disabled on pages that use this new interface, to avoid confusion. The old button will be phased out over the next few releases as we upgrade other components and make new export tools available.

Support for VCF format (all species)

Our web interface now supports two types of VCF file. Small files (up to 5MB) can now be uploaded to the website for display by selecting the "VCF" format from the dropdown menu; if you wish to attach a tabix-indexed VCF, please select "VCF (indexed)".

New species, assemblies and genebuilds

Update to Ensembl-Havana GENCODE gene set (release 20) (Human)

Updated Ensembl-Havana gene set (GENCODE release 20). This gene set is a merge of complete Ensembl gene models and the latest Havana gene annotation. All CCDS genes are included in this gene set.

The human GRCh38 gene annotation is also included.

Human: assembly updated to GRCh38 (Human)

The human genome assembly was updated to GRCh38 and the assembly information in all human databases has been altered accordingly. It consists of 24 chromosomes (1-22, X and Y), 127 unplaced scaffolds and 42 unlocalized scaffolds. This major assembly update contains 261 alt loci scaffolds (including haplotypes for the MHC region on chromosome 6 and LRC region on chromosome 19), in 35 alternate assembly units. 72 of these alternate loci were previously available as NOVEL patches to GRCh37.

Vega Mouse annotation updated (Mouse)

Manual annotation of mouse from Havana has been updated and contains the data released in Vega 56.

Vega Human annotation updated (Human)

Manual annotation of human from Havana has been updated and contains the data released in Vega 56 (GRCh38).

Other updates

Olive baboon new assembly and genebuild (Olive baboon)

We have produced a new set of gene annotations for the Panu_2,0 assembly.

Update variation data to GRCh38 (Human)

We update our variation data to the new human assembly GRCH38. New locations for our variation data are computed with methods from the Ensembl core API. 

Human: updated RefSeq gene import (Human)

The imported RefSeq gene set was updated in the human otherfeatures database. 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.

Mouse: updated RefSeq gene import (Mouse)

The imported RefSeq gene set was updated in the mouse otherfeatures database. 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.

Update to Ensembl-Havana mouse merge (Mouse)

Updated Ensembl-Havana mouse gene set. This gene set is a merge of complete Ensembl gene models and the latest Havana gene annotation. All CCDS genes are included in this gene set.

The mouse GRCm38.p2 gene annotation is also included:

The patches for GRCm37.p2 were annotated using a combination of annotation projected from the primary assembly and annotation derived from cDNA and protein alignment evidence. Annotation of the patches is stored in the core database.

Amazon molly new assembly and genebuild (Amazon molly)

We have produced a new set of gene annotations for the PoeFor_5.1.2 assembly

Amazon molly RNASeq database and Bam files (Amazon molly)

In addition to the gene annotation for PoeFor_5.1.2, an rnaseq database will be released where users can view BAM files and transcript models for 11 tissues.

Drawing code changing namespace (all species)

As part of our ongoing reorganisation of the webcode git repositories, we have moved all Bio::EnsEMBL drawing code to EnsEMBL::Draw.

This change will affect developers who have created custom drawing code tracks or components that draw images using the DrawableContainer or VDrawableContainer modules. A simple change of namespace in your code will ensure that it continues to work.

Ensembl 76 mart databases (all species)

  • Ensembl Genes 76
    • Retirement of the human expression data (eGenetics/SANBI EST and GNF/Atlas) and the zebrafish expression data (ZFIN). This will result in the removal of the "EXPRESSION" filter and attribute sections.
    • Retirement of the transcript splicing events data computed by the pipeline developed as part of the ASTD project. These data will be retired for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), zebrafish (Danio rerio), c.elegans (Caenorhabitis elegans) and fruitfly (Drosophila melanogaster). This will result in the removal of the "Transcript event" filter and attribute sections.
    • Updated human assembly to GRCh38
    • Added new species Amazon molly (Poecilia formosa) and Olive baboon (Papio anubis)
    • Added new Gene and Transcript version attributes for all the species
    • Added new Transcription Start Site (TSS) attribute in the structure and sequence sections for all the species.
    • Added "QTL chromosome name" and "QTL region" filters for sheep and chicken
    • Added marker start and end filters for sheep
  • Ensembl Variation 76
    • Updated human assembly to GRCh38
    • Added "QTL chromosome name" and "QTL region" filters for sheep and chicken
  • Vega 56
    • Updated human assembly to GRCh38
  • Ensembl Regulation 76
    • Updated human assembly to GRCh38

Human: GRCh38 Karyotype Bands (Human)

Karyotype bands were updated in all regions.

Olive baboon Otherfeatures database (Olive baboon)

Baboon-specific cDNA and ESTs along with EnsEMBL longest translations from human have been aligned to Panu_2.0. These are made available through the website and otherfeatures database.

Olive baboon RNASeq database and Bam files (Olive baboon)

In addition to the gene annotation for Panu_2.0, an rnaseq database will be released where users can view BAM files and transcript models for 14 tissues including thymus, liver, lung, heart and pituitary.

Updated human otherfeatures db: New CCDS import (Human)

This release of the human gene set also includes 29,033 transcript models as part of an updated version (April 2014) of CCDS which has been projected from assembly GRCh37.

Updated mouse otherfeatures db: New CCDS import (Mouse)

This release of the mouse gene set also includes 23,868 transcript models as part of an updated version (April 2014) of CCDS

All species: updated RefSeq sequence synonyms (all species)

The imported RefSeq sequence synonyms have been updated for all species.

Rat: Imported ncRNAs (Rat)

We have updated the set of ncRNAs for rat.

Human: updated cDNA alignments (all species)

A new cdna database was created for e75: The latest set of cDNAs for human (as of December 2013) from the European Nucleotide Archive and NCBI RefSeq (release nn) were aligned to the current genome using Exonerate.

Mouse: updated cDNA alignments (Mouse)

A new cdna database was created for e75: The latest set of cDNAs for mouse (as of January 2013) from the European Nucleotide Archive and NCBI RefSeq (release 62) were aligned to the current genome using Exonerate.

Amazon molly Otherfeatures database (Amazon molly)

EnsEMBL longest translations from human, zebrafish and stickleback have been aligned to PoeFor_5.1.2. These are made available through the website and otherfeatures database.

Retiring of GBrowse format (all species)

In release 76 we will be discontinuing support for the GBrowse file format, as it is little-used, and will be focusing in future on improving support for more popular formats.

EMBL and Genbank Dumps (all species)

EMBL and Genbank dumps for all species.

External reference projection (all species)

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

FASTA & GTF dumps (all species)

FASTA & GTF dumps for all the species

Retirement of the coreexpressionest and coreexpressionatlas databases (Zebrafish, Human)

Retirement of the following databases used to generate the data displayed in the "EXPRESSION" filter and attribute sections (eGenetics/SANBI EST and GNF/Atlas for human and ZFIN for zebrafish) of the ensembl mart:

  • danio_rerio_coreexpressionest
  • homo_sapiens_coreexpressionest
  • homo_sapiens_coreexpressionatlast

Retirement of the Alternative Splicing Event pipeline (all species)

As part of the retirement of the Alternative splicing event pipeline, we have removed the following directory from the ensembl-production git repository: ensembl-production/scripts/alternative_splicing

dbSNP updates (Cow, Chicken, Pig, Sheep)

Chicken, cow, pig and sheep will be updated to dbSNP build 140

Human Genotyping Chips update (Human)

A browser track/ variation set of variants from the Illumina Human OmniExpress-12v1 genotyping chip will be created.

New Regulatory Build (Human)

We reviewed the Build algorithm, as described in an earlier blog post. The Ensembl Regulatory Build on human is now constructed from the segmentations, to ensure consistency. In addition, the new Regulatory Build annotates the RegulatoryFeatures at the MultiCell level, each cell-type differing only by an activity variable.

New segmentations (Human)

We extended the number of segmentation to 18 celltypes, with the inclusion of cell lines A549, DND41, HMEC, HSMMT, HSMM, IMR90, Monocytes-CD14+, NHA, NHDFAD, NHEK, NHLF and Osteoblasts. The segmentations were run with Segway, at a 200bp resolution. 

FANTOM 5 enhancers and promoters (Human)

We added tables with the locations of the enhancers and promoters called by the FANTOM 5 consortium. 

JASPAR motifs (all species)

We updated the motifs to match the new release of JASPAR TF binding motifs.

Phenotype data updates (Human, Mouse)

  • Human phenotype data will be updated from different sources including ClinVar and Decipher.
  • Mouse phenotype data from IMPC will be updated.

Structural variations (multiple species)

DGVa data will be updated.

For human, the data will be projected to the new assembly (GRCh38).

Import COSMIC variants (Human)

Import COSMIC's version 69 and remap the data to GRCh38

Remove sequences and associated genes not in the assembly (Turkey)

Remove 275 sequences from the turkey assembly as they are not part of the official assembly, GCA_000146605.1.

Four genes will be deleted: ENSMGAG00000016986, ENSMGAG00000017366, ENSMGAG00000016551, ENSMGAG00000016615

Updated MT for sea squirt (C.intestinalis)

The MT was updated for sea squirt. Updating the mitochondrion annotation to NC_004447.2

LRG Import (Human)

Importing the latest version of Locus Reference Genomic dataset

patch_75_76a.sql - schema_version update in production db (all species)

Update schema_version in production database to 76.

Stable ID lookup (all species)

Stable ID lookup provided for REST services

Includes lookup for RefSeq and CCDS entries

patch_75_76_a.sql - schema_version update in ontology db (all species)

Update schema_version in meta table to 76.

External database references update (multiple species)

Xrefs update for:

human, mouse, lamprey, ciona savignyi, gorilla, tenrec, shrew, hedgehog, mouse lemur, squirrel, softshell turtle, flycatcher, rabbit, zebrafinch, dog, duck

NHLBI ESP data update (Human)

Human NHLBI ESP data will be updated to version v.0.0.26 and remapped to GRCh38

Map variations to new alternate loci in GRCh38 (Human)

We map variations to all new alternate loci in GRCh38

Sift version update (multiple species)

Sift analysis will be updated to version 5.1.0 for human, cow, chicken, horse, pig, mouse and sheep   

schema changes (all species)

The evidence column in the variation and variation_feature tables will be  replaced by an evidence_attribs column to allow configurability.

A new table 'display_group' will be added to hold information on which populations should be shown in separate tables on the PopulationGenetics page. The population table will gain an extra display_group_id to link to this table.

The read_coverage table is back in the schema (was removed in 75)

Markers from UniSTS (Sheep)

Import of the markers from SheepMap4.7 and CAB Ovine Linkage Map

ProteinTrees and homologies (all species)

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

-- all-vs-all blastp (ncbi-blast-2.2.27+)
-- Clustering using hcluster_sg
-- Multiple sequence alignments using MCoffee (Version_9.03.r1318) or Mafft (mafft-7.017)
-- 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 (all species)

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 (all species)

New pipeline that makes the Families consistent with the gene-trees. It includes all the Ensembl transcript isoforms (including human non-reference haplotypes) and newest Uniprot Metazoa.

Clustering using the TreeFam 10 HMM library

Multiple Sequence Alignments with MAFFT (v.7.017)

Family stable ID mapping

API/Schema changes (all species)

- Several objects now inherit from Storable (methods: dbID(), adaptor(), new_fast(), new())

- Methods scheduled for deletion in e76 have been removed

- Split member into seq_member and gene_member + members depend on dnafrags

lastz alignments (all species)

lastz H.sap-C.hof (on H.sap)  ( choloepus_hoffmanni, homo_sapiens ) 

lastz H.sap.O.ari (on H.sap) ( ovis_aries, homo_sapiens )

lastz H.sap-C.por (on H.sap)  ( cavia_porcellus, homo_sapiens )

lastz H.sap-D.nov (on H.sap)  ( dasypus_novemcinctus, homo_sapiens )

lastz H.sap-D.ord (on H.sap)  ( dipodomys_ordii, homo_sapiens ) 

lastz H.sap-E.eur (on H.sap)  ( erinaceus_europaeus, homo_sapiens )

lastz H.sap-E.tel (on H.sap)  ( echinops_telfairi, homo_sapiens )

lastz H.sap-L.afr (on H.sap)  ( homo_sapiens, loxodonta_africana )

lastz H.sap-M.eug (on H.sap)  ( homo_sapiens, macropus_eugenii )

lastz H.sap-M.mur (on H.sap)  ( microcebus_murinus, homo_sapiens )

lastz H.sap-O.pri (on H.sap)  ( ochotona_princeps, homo_sapiens )

lastz H.sap-P.cap (on H.sap)  ( procavia_capensis, homo_sapiens )

lastz H.sap-P.vam (on H.sap)  ( pteropus_vampyrus, homo_sapiens )

lastz H.sap-S.ara (on H.sap)  ( sorex_araneus, homo_sapiens )

lastz H.sap-T.bel (on H.sap)  ( tupaia_belangeri, homo_sapiens )

lastz H.sap-T.syr (on H.sap)  ( tarsius_syrichta, homo_sapiens )

lastz H.sap-T.tru (on H.sap)  ( tursiops_truncatus, homo_sapiens )

lastz H.sap-V.pac (on H.sap)  ( vicugna_pacos, homo_sapiens )

lastz H.sap-I.tri (on H.sap)  ( homo_sapiens, ictidomys_tridecemlineatus )

lastz H.sap-M.fur (on H.sap)  ( homo_sapiens, mustela_putorius_furo ) 

lastz H.sap-M.luc (on H.sap)  ( homo_sapiens, myotis_lucifugus ) 

lastz H.sap-A.mel (on H.sap)  ( homo_sapiens, ailuropoda_melanoleuca )

lastz H.sap-E.cab (on H.sap)  ( equus_caballus, homo_sapiens )

lastz H.sap-M.dom (on H.sap)  ( monodelphis_domestica, homo_sapiens )

lastz H.sap-O.ana (on H.sap)  ( ornithorhynchus_anatinus, homo_sapiens )

lastz H.sap-B.tau (on H.sap)  ( homo_sapiens, bos_taurus )

lastz H.sap-C.fam (on H.sap)  ( homo_sapiens, canis_familiaris )

lastz H.sap-C.jac (on H.sap)  ( homo_sapiens, callithrix_jacchus ) 

lastz H.sap-F.cat (on H.sap)  ( homo_sapiens, felis_catus ) 

lastz H.sap-G.gor (on H.sap)  ( homo_sapiens, gorilla_gorilla ) 

lastz H.sap-M.mul (on H.sap)  ( macaca_mulatta, homo_sapiens )

lastz H.sap-M.mus (on H.sap)  ( homo_sapiens, mus_musculus )

lastz H.sap-N.leu (on H.sap)  ( homo_sapiens, nomascus_leucogenys )

lastz H.sap-O.cun (on H.sap)  ( homo_sapiens, oryctolagus_cuniculus )

lastz H.sap-O.gar (on H.sap)  ( homo_sapiens, otolemur_garnettii )

lastz H.sap-P.abe (on H.sap)  ( homo_sapiens, pongo_abelii )

lastz H.sap-P.tro (on H.sap)  ( homo_sapiens, pan_troglodytes )

lastz H.sap-R.nor (on H.sap)  ( homo_sapiens, rattus_norvegicus )

lastz H.sap-S.har (on H.sap)  ( homo_sapiens, sarcophilus_harrisii )

lastz H.sap-S.scr (on H.sap)  ( homo_sapiens, sus_scrofa )

lastz H.sap-A.pla (on H.sap)  ( homo_sapiens, anas_platyrhynchos )

lastz H.sap-F.alb (on H.sap)  ( homo_sapiens, ficedula_albicollis )

lastz H.sap-G.gal (on H.sap)  ( homo_sapiens, gallus_gallus )

lastz H.sap-P.sin (on H.sap)  ( homo_sapiens, pelodiscus_sinensis )

lastz H.sap (on H.sap) ( homo_sapiens )

lastz C.sav-H.sap (on H.sap) ( ciona_savignyi,homo_sapiens )

lastz H.sap-A.car (on H.sap) ( homo_sapiens,anolis_carolinensis )

lastz H.sap-C.int (on H.sap) ( homo_sapiens,ciona_intestinalis )

lastz H.sap-D.rer (on H.sap) ( homo_sapiens,danio_rerio )

lastz H.sap-G.acu (on H.sap) ( gasterosteus_aculeatus,homo_sapiens )

lastz H.sap-G.mor (on H.sap) ( homo_sapiens,gadus_morhua )

lastz H.sap-L.cha (on H.sap) ( homo_sapiens,latimeria_chalumnae )

lastz H.sap-O.lat (on H.sap) ( oryzias_latipes,homo_sapiens )

lastz H.sap-O.nil (on H.sap) ( homo_sapiens,oreochromis_niloticus )

lastz H.sap-P.mar (on H.sap) ( homo_sapiens,petromyzon_marinus )

lastz H.sap-T.gut (on H.sap) ( taeniopygia_guttata,homo_sapiens )

lastz H.sap-T.nig (on H.sap) ( tetraodon_nigroviridis,homo_sapiens )

lastz H.sap-T.rub (on H.sap) ( takifugu_rubripes,homo_sapiens )

lastz H.sap-X.mac (on H.sap) ( homo_sapiens,xiphophorus_maculatus )

lastz H.sap-X.tro (on H.sap) ( homo_sapiens,xenopus_tropicalis ) 

lastz M.gal-H.sap (on H.sap) ( homo_sapiens,meleagris_gallopavo )

lastz M.mus-C.por (on M.mus) ( mus_musculus,cavia_porcellus )

lastz C.fam-F.cat (on C.fam) ( canis_familiaris,felis_catus )

lastz C.fam-M.fur (on C.fam) (canis_familiaris,mustela_putorius_furo )

lastz M.mus-S.ara (on M.mus) ( mus_musculus,sorex_araneus)

lastz B.tau-T.tru (on B.tau) (bovis_taurus,tursiops_truncatus)

lastz B.tau-F.cat (on B.tau) (bovis_tarurus,felis_catus)

lastz B.tau-M.fur (on B.tau) (bovis_taurus,mustela_putorius_furo)

lastz B.tau-P.vam (on B.tau) (bovis_taurus,pteropus_vampyrus)

lastz H.sap-P.anu (on H.sap) (homo_sapiens, papio_anubis)

lastz H.sap-C.pyg (on H.sap) (homo_sapiens, chlorocebus pygerythrus)

lastz G.gal-M.dom (on G.gal) (gallus_gallus,monodelphis_domestica)

lastz O.lat-M.mus (on O.lat) (oryzias_latipes, mus_musculus)

Syntenies (all species)

H.sap-M.dom (on H.sap)

H.sap-O.ana (on H.sap)

H.sap-B.tau (on H.sap) 

H.sap-C.fam (on H.sap) 

H.sap-E.cab (on H.sap)

H.sap-M.gal (on H.sap)

H.sap-C.jac (on H.sap)

H.sap-F.cat (on H.sap)

H.sap-G.gor (on H.sap)

H.sap-M.mul (on H.sap)

 H.sap-M.mus (on H.sap)

H.sap-O.cun (on H.sap)

H.sap-P.tro (on H.sap)

H.sap-R.nor (on H.sap)

H.sap-S.scr (on H.sap) 

H.sap-G.gal (on H.sap)

H.sap-A.car (on H.sap)

H.sap-D.rer (on H.sap)

H.sap-G.acu (on H.sap) 

H.sap-O.lat (on H.sap)

H.sap-T.gut (on H.sap) 

H.sap-T.nig (on H.sap)

C.fam-F.cat (on C.fam)

B.tau-F.cat (on B.tau)

H.sap-O.ari (on H.sap)

HGMD data update (Human)

Import of the latest release of public HGMD data (version 2013.4 from December 2013) and remapping to GRCh38

Gencode Track (Human, Mouse)

To have a separate track for Gencode splitting the current Gencode 20 to Gencode 20 comprehensive and Gencode basic. Available for human and mouse only.

Retitrement of archives 62 and 63 (all species)

This release cycle we will be retiring archive 62 (April 2011) and 63 (June 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.

Platyfish MT contig removal (Platyfish)

The Platyfish assembly has contigs from the Mitochondial chromosome labelled as toplevel sequence. The MT contigs do not form the MT scaffold in the platyfish assembly as stored in the database, and will be deleted.

patch_75_76_a.sql - schema_version update (all species)

Update schema_version in meta table to 76.

patch_75_76_b.sql - allow null karyotype (all species)

Band and stain column in karyotype table can be null

Ensembl VM Build (all species)

The Ensembl Virtual Machine applicance will be updated to version 76.

Includes a larger disk space for VEP compatibility

patch_75_76_c.sql - alternative splicing event retirement (all species)

Remove splicing event tables which are not used any more.

Retirement of splicing event related material (all species)

Match the removal of the splicing_event tables, by retiring the corresponding modules:

- Bio::EnsEMBL::DBSQL::SplicingEventAdaptor

- Bio::EnsEMBL::DBSQL::SplicingEventFeatureAdaptor

Bio::EnsEMBL::DBSQL::SplicingTranscriptPairAdaptor

- Bio::EnsEMBL::SplicingEvent

- Bio::EnsEMBL::SplicingEventFeature

- Bio::EnsEMBL::SplicingTranscriptPair

Archive of previous news

Future Plans

Read about our future plans on our blog!