Follow up on Nov 2015 Webinar: Variant Effect Prediction using the standalone perl scripts

In  November 2015 Gramene Webinar, Matt Geniza, (a graduate student, Jaiswal Lab at Oregon State University) presented how to use standalone Perl script and command line protocols for Variant Effect Predictor (VEP) analysis. This option is for advanced users who are familiar with the Unix/Linux command line. Also, users are expected to have a SNP DATA file before proceeding for this exercise.

Announcing Gramene database build 48b highlighting Plant Reactome

The Gramene project ( team is pleased to announce its release #48b highlighting the new version of Plant Reactome database ( In this release the Plant Reactome database has expanded gene homology-based pathway projections to 58 plant species.

GARNet/Egenis Workshop on Big Data: April 2016

Click on the link below to view the full schedule for the GARNet/Egenis workshop on 'Integrating Large Data into Plant Science: From Big Data to Discovery'.

Detailed schedule as PDF

This will take place in Dartington Hall, Totnes, Devon UK. There are a limited number of places available for delegates so anyone interested in attending should contact with details as to why this meeting would be beneficial for your research.

Gramene at Programming for Biology 2015

The Gramene group continued a long-standing tradition of teaching and support at Cold Spring Harbor Laboratory's Programming for Biology taught course led by Simon Prochnik and Sophia Robb that ran October 11-27th 2015.


Gramene at Genome Informatics 2015

Genome Informatics was held at Cold Spring Harbor Laboratories from October 28-31. From the CSHL meetings page

Gramene database build 48 released

The Gramene Team is pleased to announce its release #48. In collaboration with Ensembl Plants we are providing in this release:

  • New ATLAS gene expression annotations

  • New pairwise alignment between Solanum tuberosum and S. lycopersicum (build 2.50)

  • New pairwise alignments between Theobroma cacao and: 1) Arabidopsis thaliana, 2) Oryza sativa, and 3) Vitis vinifera

The 13th International Symposium on Rice Functional Genomics

The 13th International Symposium on Rice Functional Genomics (ISRFG) conference was organized by the National Key Laboratory of Crop Genetic Improvement at Huazhong Agricultural University in Wuhan, China, from the 21st to the 24th of September 2015.


Prof. QIFA ZHANG welcoming 13th ISRFG participants (Photo credit : Organizers of 13th ISFRG)

Gramene BLAST Webinar on Tues, Oct 20, 2015 @ 2:00 pm EDT

Have a BLAST with Gramene!

The Gramene database invites you to a FREE 30-min webinar on Gramene BLAST.

This webinar will highlight important features of the sequence BLAST tool and demonstrate how to maximize your chances of getting the best BLAST hits. The tool allows aligning query sequences against genomic DNA, cDNAs and translated peptides of 39 plant genomes in Gramene.

New Plant Ontology Release available

A new Plant Ontology (PO) data release is available on the PO browser.

See the highlights in the PO's News blog and complete details in PO's release notes.


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