[Gramene-announce] Gramene database build 40 released -- Check out our new look!

[Monaco, Marcela]

The Gramene Team is pleased to announce its release #40.


Website
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You'll notice we have a new look --- You can find all the old stuff at Gramene's Archive<http://archive.gramene.org<http://archive.gramene.org/>>.

Gramene’s new search is powered by the Apache Solr search engine and is significantly faster than previous versions which used MySQL.  The search tool allows users to search by keyword and then drill down into the search results by species, object type (e.g., gene, pathway), and associated ontology terms.

The Gramene genome browser, database schema and API have been updated to Ensembl version 74<http://useast.ensembl.org/info/docs/api/index.html>.


Genomes
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In collaboration with Ensembl Plants we are providing in this release:

* MSU7 gene models for rice so that both MSU7 and IRGSP models can be visualized in a single frame of the genome browser
* Mappings between the MSU and IRGSP gene sets from RAP-DB<http://rapdb.dna.affrc.go.jp/> allowing searching and
querying using either identifier
* The chromosome survey sequence for bread wheat  (Chinese Spring) generated by IWGSC<http://www.wheatgenome.org/>, as well as over 100,000 protein-coding wheat genes predicted by MIPS<http://mips.helmholtz-muenchen.de/plant/wheat/iwgsc/index.jsp>
* Functional annotation, genome alignments, and inferred evolutionary histories for bread wheat
* Additional wheat RNA-Seq data
* DNA-DNA alignments between wheat, rice, and Brachypodium
* Updated gene-trees to include wheat gene models
* Updated GO terms for rice and their projections to other species
* Updated repeat analysis (TREP) for wheat genomes


Pathways
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In a joint effort with MaizeGDB, we have added new GO associations to MaizeCyc version 2.2<http://pathway.gramene.org/maizecyc.html>.



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 to improve Gramene's new site.

We value and welcome your Feedback!!!


The Gramene Team


==
Marcela Karey Monaco, PhD
Gramene Project Coordinator
Cold Spring Harbor Laboratory