Gramene database build 50 released

Submitted by marcela.karey on Thu, 04/07/2016 - 16:11

The Gramene Team is pleased to announce its release #50. In collaboration with Ensembl Plants, we are providing in this release:

  • New variation data for Oryza sativa japonica
  • New orthologous-based pathway projections for Eucalyptus grandis, Jatropha curcas, Manihot esculenta, and Mimulus guttatus in the Plant Reactome
  • Newly curated rice pathways in the Plant Reactome 
  • New Plant Reactome cross-references for all 39 plant genomes
  • 
New ncRNA alignments across all 39 genomes
.
    • To view these for your species of interest, select a region by going to Location View => Configure Region Image => Sequence assembly => GRC alignments => select Rfam models
  • New track hubs for more than 900 public RNA-Seq studies, totaling more than 16,000 tracks across 35 plant species
  • Updated putative split gene annotation artifacts

  • Updated protein domain information based on the latest InterProScan
  • New HMMER tool for fast protein sequence search using Hidden Markov Models
  • Updated gene and variation BioMarts
  • Searches within ensembl.gramene.org are now being served by our new search API hosted at data.gramene.org

  • Updated software, genome browser, database schema and API to Ensembl v84 software

A complete description of the contents of this new release is available in our release notes.

Please let us know if you have questions or suggestions.

The Gramene Team