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News for Ensembl Release 90

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New web displays and tools

Scaling custom tracks (all species)

In this release we have added the ability to adjust the y-axis of your "wiggle" tracks, such as BigWig and bedGraph files. This feature is available in two places on the website:

  1. When you upload a bedGraph file or attach a BigWig, you will have the option to set the minimum and maximum values for the y-axis (as well as the colour of the graph)
  2. Once the track is displayed, you will be able to change the values by clicking on the track name in the left-hand edge of the image and using the popup menu - the tab is marked by a histogram icon (see screenshot, below).

Disconnecting and reconnecting track hubs (all species)

Many track hubs have a lot of tracks, and if you want to configure which tracks are shown it can take quite a while. And if you delete the hub from your Ensembl session and then add it back, you have to go through the whole process all over again!

To save time and effort, you can now disconnect the track hub from the browser and then reconnect it later without losing your configuration changes. In the 'Your Data' table there is now a disconnect/reconnect icon - just click on it and then close the control panel to update the genome browser.

Note that if you want to be able to reconnect a hub with the same settings whilst on a different computer, you will need to save the configuration to your Ensembl account.

New species, assemblies and genebuilds

New rodent species (multiple species)

In this release we are adding 12 new rodent species to Ensembl (including three species that were formerly available on our Pre site), and updating three existing non-murine species (guinea pig, squirrel and kangaroo rat). The new genomes are:

  • Cavia aperea (Brazilan guinea pig)
  • Chinchilla lanigera (Long-tailed chinchilla)
  • Cricetulus griseus (Chinese hamster) - 2 cell lines
  • Fukomys damarensis (Damara mole rat)
  • Heterocephalus glaber female (Naked mole rat) - male and female
  • Jaculus jaculus (Lesser Egyptian jerboa)
  • Mesocricetus auratus (Golden hamster)
  • Microtus ochreogaster (Prairie vole)
  • Mus caroli (Ryukyu mouse)
  • Mus pahari (Shrew mouse)
  • Nannospalax galili (Upper Galilee mountains blind mole rat)
  • Octodon degus (Degu)
  • Peromyscus maniculatus bairdii (North American deer mouse)

New genome annotation on the pig assembly Sscrofa11.1 (Pig)

New genome annotation of the new pig assembly Sscrofa11.1, GCA_000003025.6, based on a comprehensive set of species specific RNA-Seq data, PacBio long reads, cDNAs and vertebrate proteins

Mouse: update to Ensembl-Havana GENCODE gene set (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.

Update to Ensembl-Havana human GENCODE gene set (release 27) (Human)

Updated Ensembl-Havana gene set (GENCODE release 27). 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.p10 gene annotation is also included:

The patches for GRCh38.p10 were annotated using a combination of manual annotation, 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.

Mouse: updated cDNA alignments (all species)

A new cdna database will be created for e89: The latest set of cDNAs for mouse (as of April 2017) from the European Nucleotide Archive and NCBI RefSeq will be aligned to the current genome using Exonerate.

Mouse: updated cDNA alignments (Mouse)

A new cdna database will be created for e90: The latest set of cDNAs for mouse (as of June 2017) from the European Nucleotide Archive and NCBI RefSeq will be aligned to the current genome using Exonerate.

Human: updated cDNA alignments (Human)

A new cdna database will be created for e90: The latest set of cDNAs for human (as of June 2017) from the European Nucleotide Archive and NCBI RefSeq will be aligned to the current genome using Exonerate.

Add transcript models from new RNAseq to zebrafish core set (Zebrafish)

New transcript and gene models will be added to the zebrafish core gene set that were produced from new developmental RNAseq data from WTSI.

New zebrafish pri-miRNAs (Zebrafish)

Zebrafish pri-miRNA transcript models are being imported into the zebrafish otherfeatures database for e90 so that they can be viewed in the browser.

New regulation data

Microarray Probe Mapping Update (multiple species)

Update probe mappings for all species with a funcgen db inclusing mouse strains

New probe mapping data for five new rodents (Guinea Pig, Golden Hamster, Upper Galilee mountains blind mole rat, Chinese hamster CHOK1GS, Chinese hamster CriGri)

Probe mappings for five new rodents are available in release 90.

New alignments

New external data for the pig genome (Pig)

New database containing all the cDNAs and the PacBio long reads alignments

Other updates

Compara

ncRNAtrees and homologies (all species)

  • Classification based on Rfam models (v12.1)
  • Multiple sequence alignments with Infernal
  • Phylogenetic reconstruction using RAxML
  • Phylogenetic reconstruction using FastTree2 and ExaML 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

patch_89_90_a.sql - Schema version update (all species)

89 -> 90

Protein Families (all species)

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

 -- Clustering by PantherScore (based on Ensembl HMM library)
 -- Multiple Sequence Alignments with MAFFT (v.7.221)

ProteinTrees and homologies (all species)

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

 -- all-vs-all blastp (ncbi-blast-2.2.30+)
 -- Clustering using hcluster_sg
 -- Multiple sequence alignments using MCoffee (Version_9.03.r1318) or Mafft (mafft-7.221)
 -- 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)

 -- computation of pairwise gene-order conservation score

 -- comparison of orthologies with whole-genome alignments

 -- high-confidence calls

 -- use of cd-hit to remove redundancy in blast db

patch_89_90_e.sql - new seq_member_projection and seq_member_projection_stable_id table (all species)

  • To hold information about projected members
  • Required by mouse strains and cd-hit implementation
  • allows for a representative sequence to be used in both blast and HMM classification and its resultant data to be projected onto other members of the cluster for expediency

S.scrofa alignments (all species)

We will compute LastZ alignments for new pig assembly:

  • pig v cow
  • pig v sheep
  • human v pig
  • mouse v pig

Recompute multiple alignments (all species)

EPOs containing updated species should be recomputed:

  • mammals

Pecan alignments:

  • amniotes (only to update new assemblies)

Mouse alignments (all species)

We will compute LastZ alignments for new mice, mus caroli and mus pahari

  • caroli v mouse
  • pahari v mouse
  • caroli v human
  • pahari v human

For consistency we will also align mus spretus against the reference mouse

patch_89_90_b.sql - DB Schema update:genomic_align_tree.parent_id (all species)

allow NULL in genomic_align_tree.parent_id

patch_89_90_c.sql - Mark constrained_element.p_value as NOT NULL (all species)

This will also fix a bug in the code whereby pvalue=0 was stored as NULL. From now on, p-values are always defined and 0 will be used

patch_89_90_d.sql - Allow NULL in genomic_align_tree.left_node_id/right_node_id (all species)

NULL was previously not allowed and led to 0 being used

patch_89_90_f.sql - Add missing biotype-groups in the gene_member table (all species)

The list of biotype groups was missing a few ones like "pseudogene", but also other genes that are meant to be ignored but need to be loaded for consistency

LastZ alignments: rodent collection (all species)

All the new rodents will be aligned against human and mouse with LastZ

Chinese Hamster Ovary Cell Line alignments (all species)

We will import the alignment with mouse computed by Eagle Genomics and will compute the alignment against human

Core

External database references update (all species)

Xrefs updates for: homo_sapiens (human), mus_musculus (mouse), rattus_norvegicus (rat), sus_scrofa (pig)

Regulation

Schema patches (all species)

patch_89_90_a.sql - Update schem_version in meta table to 90

patch_89_90_b.sql - Track the sequence type (genomic or a transcript) and id (seq region name or stable id) of the sequence on which a probe feature was found

patch_89_90_c.sql - Add stable id index to the probe_transcript table to speed up generation of the transcript pages on the website

patch_89_90_d.sql - Add stable id index to the probe_set_transcript table

Genebuild

Updated human otherfeatures db: New CCDS import (Human)

This release of the human gene set also includes 32,512 transcript models as part of an updated version (April 2017) of CCDS.

New RNA-Seq database for the pig annotation (Pig)

New RNA-Seq database containing the models for all the different tissue samples of PRJEB19386

Annotation of Horizon Chinese hamster ovary cell line assembly by Eagle Genomics (Chinese hamster CHOK1GS)

Eagle Genomics have created a gene annotation for the Horizon Chinese hamster ovary cell line assembly using the Ensembl gene annotation pipeline.

import annotations for caroli and pahari (Shrew mouse, Ryukyu mouse)

importing annotations of 2 mouse species. 

Annotation of Chinese hamster ovary cell line assembly (Chinese hamster CriGri)

We have produced gene annotation for Chinese Hamster ovary cell line assembly

Production

Ensembl 90 mart databases (all species)

  • Ensembl Genes 90
    • Addition of new rodents, Mus Caroli, Pahari and Spretus
    • Addition of new versioned stable ID filter/attribute for Gene, Transcript and Translation
    • Retired Status filters and attributes
  • Mouse Genes 90
    • Moved Mus Spretus to Ensembl Genes mart 90
    • Retired Status filters and attributes
  • Ensembl Variation 90
  • Ensembl Regulation 90

Future Plans

Read about our future plans on our blog!