News for Stickleback Ensembl Release 89 (May 2017)

News categories

Compara

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

Core

External database references update

Xrefs updates for: homo_sapiens (human), mus_musculus (mouse), danio_rerio (zebrafish), loxondonta africana (elephant), notamacropus eugenii (wallaby), papio anubis (olive baboon), ochotona princeps (pika), procavia capensis (hyrax), pteropus vampirus (megabat), tupaia belangeri (tree shrew), anas platyrhynchos (duck), dasypus novemcinctus (armadillo), ictidomys tricemlineatus (squirrel), gasterosteus aculeatus (stickleback)

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.

Production

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