News for Medaka Ensembl Release 89 (May 2017)

News categories


ncRNAtrees and homologies

  • 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_88_89_a.sql - Schema version update

88 -> 89

Protein Families

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

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


GO terms for transcripts

GO terms have been introduced for some miRNAs. As a result, GO terms are now linked to transcripts rather than translations.


Ensembl 89 mart databases

  • Ensembl Genes 89
    • Updated Microarray probes/probesets for all the species
    • Dataset "meugenii_gene_ensembl" was renamed to "neugenii_gene_ensembl"
    • Dataset "tsyrichta_gene_ensembl" was renamed to "csyrichta_gene_ensembl"
    • GO and GOSlim terms were moved from Translation to Transcript
  • Mouse Genes 89
    • Microarray probes/probesets added for all the mouse strains
    • GO and GOSlim terms were moved from Translation to Transcript
  • Ensembl Variation 89
    • New filters for regulatory and motif consequence types
  • Ensembl Regulation 89
    • Updated VISTA Enhancers for human and mouse

About this species