News

American Journal of Botany

New search tools give scientists better ways of managing data

The BBSRC funded Wheat Improvement Strategic Programme (WISP, http: //www.wheatisp.org ) 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 release 35 includes variation data for Zea mays (maize) and Oryza glaberrima (African rice). The new maize variation data corresponds to the HapMap v2 set and comprises 55 million SNPs and indels identified in a collection of 103 pre-domesticated and domesticated Zea mays varieties, including a representative from the sister genus, Tripsacum dactyloides (Eastern gamagrass).

Putative gene split models are available for 18 plant reference genomes hosted at Gramene. The split gene models are commonly related to an annotation artifact wherein a single gene is annotated as two or more genes due to incomplete evidence, but could also result from legitimate evolutionary processes. The Compara Gene Tree method predicts a special class of within-species paralogs called "contiguous_gene_split". A contiguous_gene_split is called when the two apparently paralogous genes lie on the same strand and in close proximity (<1MB) but have no (or little) overlapping sequence.

Left to right: Donghui Li (TAIR), Laurel Cooper (Plant Ontology), Sylva Donaldson (BAR), Steve Goff (iPlant), Kate Dreher (PMN), Eva Huala (TAIR), Doreen Ware (Gramene), and Ken Youens-Clark (Gramene). Josh Stein (Gramene & iPlant) who contributed this blog, is missing in this group photo.

Visit our Plant Genome Resources Outreach Booth #215 at the annual Plant Biology meeting of the ASPB to meet representatives of Gramene, PMN, PO/TO, BAR, TAIR, iPlant, and KBase. A complete schedule for the booth is available here. Also available at the booth are brochures for MaizeGDB, SoyKB, and SolGenomics.

Gramene will be present at this week's Plant Biology 2012, the Annual Meeting of the American Society of Plant Biologists (ASPB), in Austin, TX from July 20-24, 2012. On Saturday, July 21, Principal Investigator Doreen Ware will present an overview of Gramene in the Plant Informatics Workshop from 7:30-10:30 PM.

EMBL-EBI is organizing a hands on phytopathology training course for PhD and post-doc researchers who are working on all aspects of fungal and oomycete-induced disease in plants at Hinxton, Cambridge, UK on 19-20 September, 2012.  This course will provide an overview with the toolset and data available for analysis of host and pathogen genomes, and infectious phenotypes.

Many users download the TASSEL standalone zip distributions instead of using the web site launch links.  This is primarily, so that the maximum heap size available to the application can be increased (by editing either start_tassel.pl or run_pipeline.pl).

The 23rd ICAR will be taking place at the Hofburg Imperial Palace in Vienna, Austria on July 3-7, 2012.  This annual conference is the largest gathering of scientists working on Arabidopsis.  It is expected that over 800 participants from around the world will attend.