Website

See also legacy data in the Gramene's Archive.

Genomes Release Notes

• New data

  • New ATLAS gene expression annotations. See an example Gene summary page
  • New pairwise alignment between Solanum tuberosum and S. lycopersicum (build 2.50)
  • New pairwise alignments between Theobroma cacao and:
    • Arabidopsis thaliana, and
    • Oryza sativa, and
    • Vitis vinifera
  • Extensive new pairwise alignments between the 12 OGE species, covering nearly 50 pairs of species, e.g.
    • O. barthii vs. O. rufipogon,
    • O. meridionalis vs. O. sativa, and
    • O. barthii vs. Leersia perrieri
  • Updated repeat identification across all plant species using RepBase (release 20140131) and PGSB-REdat (release 9.3p)

• Updated data

  1. Updated to Ensembl 82 software
  2. Updated BioMarts
  3. Updated protein domain information based on latest InterProScan
  4. Updated pairwise alignments between Hordeum vulgare and:
     • Aegilops tauschii,
     • Brachypodium distachyon, and
     • O. sativa

Genomes Core

Ensembl Variation

Compara

Gene Trees

• The EnsemblCompara GeneTree database was updated. The new database includes a total of 56,387 GeneTree families were constructed comprising 1,280,368 individual genes (1,432,406 input proteins) from 39 plant genomes (and 5 non-plant outgroups).

• The OGE Compara tree was not updated at oge.gramene.org. Last update was done in release 38 (August 2013). Note: The OGE Compara tree was pulled out from the website since they were build on the obsolete MSU6 genome assembly.

Potential gene annotation artifacts

For a complete list, see Gramene's FTP site. Summary statistics follow.

Split genes by species

Synteny

No new synteny data was generated for this release. Last update was done in release 39 (October 2013).

WGA and other nucleotide alignments

Updated whole genome alignments for S. lycopersicum vs A. thaliana, O. sativa Japonica, and V. vinifera.

Protein Annotation, Go, Xref

UniProtKB cross-references were updated across all species.

Mart

New Plant Gene and Plant Variation Marts

Pathway Release Notes

"Cyc" Pathways

• BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at iPlant.

Summary tables for the Cyc pathway databases created by Gramene can be seen in release 46 notes.

Ontologies Release Notes

No updates in this release. Last update done in release 31 (May 2010). A summary of ontologies data was last provided in release 46.

Infrastructure

Web Services

Gramene's web services page documents many ways to directly connect to and analyze our databases.

Programmatic access to Gramene is now available through the RESTful Ensembl API.

Public MySQL Server

Our partner Ensembl Genomes offer a public, read-only MySQL server with copies of the species-specific and comparative genomic databases that we use. To use this with the mysql command-line client:

$ mysql -hmysql-eg-publicsql.ebi.ac.uk -P4157 -uanonymous

Please note that the versioning scheme used at this public database differs from ours; Gramene's release 48_82 is set as version 29_82.

Gramene currently a legacy public, read-only MySQL server for release 40 of our databases. You can connect to the host "gramenedb.gramene.org" with the password "gramene," e.g.:

mysql -hgramenedb.gramene.org -pgramene