News

Gramene database build 39 released

The Gramene Team is pleased to announce its release #39. In collaboration with Ensembl Plants we are providing in this release:

DNA Biology and Bioinformatics summer camp for high school students at Oregon State University

“Did you know that there are millions of DNA building blocks encoded in the genome of a plant? How can scientists possibly study this vast amount of data? With computers! Come and explore the tools of modern biology used to examine the complexities of DNA. This camp will involve hands-on activities where you will extract genetic material from a plant, assemble DNA sequences, identify genes using computers, examine your plant’s genome with visualization software, and test and look at your results in the laboratory. No programming skills required!”

Updates to the Zea mays reference assembly

Since publishing the initial assembly of the reference strain (B73) in 2008, the maize sequencing project has released two updates. The initial assembly and RefGen_v2 are based on a BAC (bacterial artificial chromosome) sequencing strategy. RefGen_v2 included ~2000 updated BAC sequences and improved upon the initial assembly by resolving overlaps between BACs in the minimum tiling path to define the 10 chromosome pseudomolecules.

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Improved GRMZM5G891969 gene model. A denovo contig provided two missing exons needed to merge two apparently distinct gene models (GRMZM5G823855 and GRMZM5G891969) into a single model that is conserved in sorghum (Sb01g050450).

Deprecation of maizesequence.org

The maize sequencing project had been running an EnsEMBL based genome browser, comparative analysis tools, and biomart at maizesequence.org, but this responsibility been transferred to gramene.org. Gramene hosts the current maize B73 reference genome sequence (RefGen_v3) and annotations along with regularly updated database cross references and comparative analyses provided by Gramene and collaborators at plants.ensembl.org.

Immediate Opening for a Pathway Biocurator Job/Position

Immediate opening is available for a recent PhD graduate (0-3 years after PhD award) to apply for a full-time postdoctoral scholar position. The biocuration would involve to annotating plant metabolic, signaling and regulatory pathways for developing an online Plant Pathway database. The curator will be responsible for

GRCN-2013 Highlights

The Grape Research Coordination Network (GRCN)-2013 meeting was held in UC Davis, from July9-12, 2013.  About 70 participants including scientists, postdocs, graduate and undergraduate students attended this meeting.  Several groups in the grape community are generating high-throughput genomic data sets and need a bioinformatics infrastructure.  Several grape researchers use Gramene's genome portal, especially the grape genome browser and are very positive about the functionality of this portal. They view Gramene as a model database for organizing various genomic and genetic resources.

Gramene database build 38 released

The Gramene Team is pleased to announce its release #38.  In collaboration with Ensembl Plants we are providing in this release:

Introduction to Pathways and Gene Expression Analysis at Gramene

Gramene currently hosts ten species-specific Pathways Databases; RiceCyc (Oryza sativa japonica), SorghumCyc (Sorghum bicolor), MaizeCyc (Zea mays), BrachyCyc (Brachypodium distachyon), AraCyc(Arabidopsis thaliana), MedicCyc(Medicago truncatula), PoplarCyc(Populus trichocarpa), CoffeaCyc(Coffea canephora), LycoCyc(Solanum lycopersicum

WISP course on Wheat Genetics at the John Innes Centre, Norwich, UK on November 18-21, 2013

The BBSRC funded Wheat Improvement Strategic Programme (WISP) aims to identify new and useful genetic variation to support the vital contribution of wheat breeding to food security. The aim of this course is to offer training in the genetic analysis methodologies employed in WISP at the John Innes Centre. The participants will gain the skills necessary to apply these methodologies in their own research.

Gramene at ASPB's Plant Biology 2013

Gramene is looking forward to participating at the annual ASPB's Plant Biology meeting in the Rhode Island Convention Center in Providence from July 20-24, 2013.  We invite the community of plant researchers and breeders to learn how to get the most out of our resources by joining the Genomic Tools mini-symposium, one of our posters (P25019 and P15030) or stop by the genomic resources Outreach Booth #200.  See you soon in the "Ocean state"!

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