The Gramene Database build 57 is out with a new polyploid genomes view!

Submitted by marcela.karey on Thu, 05/03/2018 - 17:56

The Gramene Team is pleased to announce its release #57 with 2,076,020 genes and 53 reference plant genomes.  Among the genes in this release, 1,892,629 are protein coding.  In turn 1,703,219 protein-coding genes are organized in 67,042 gene family trees.

  • New features:
    • New in this release is the polyploid view for wheat, which allows users to view alignments between all 3 wheat (A, B and D genome) components simultaneously.
    • SIFT scores are now displayed on the 'Genes and regulation' view of a gene variant. Here is a sorghum SNP.  Note: Users can also filter SNP variants by SIFT score in the Gramene Mart.
  • Updated data:
    • Added gene name synonyms for O. sativa using from database sources such as CGSNL, Oryzabase and Rap-DB.
    • Updated protein features for all (nearly 2 million) plant proteins using InterProScan with version 67 of InterPro.
    • Updated BioMarts for all gene and variation data.
    • 26 new and updated functional genomic databases (example for Arabidopsis).
    • Tandem repeats annotated by the TRF program are no longer used to soft- and hardmask the genome sequences. This affects sequences retrieved via the API and the files on the FTP site.
  • Updated software:

Feature highlight: Users can download individual sample genotypes for selected genomes (e.g., sorghum, barley, grape, and Oryza glaberrima) via Gramene's Mart.

This release would not have been possible without a complete Ensembl software update to v92.  A complete description of the contents of the release is available in our release notes.  The genome databases were built in direct collaboration with Ensembl Plants and the Plant Reactome database was maintained in collaboration with the Reactome project.

Please let us know if you have questions or suggestions.

The Gramene Team