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Latest update: March 12, 2010

PlantGDB at Maize Genetics Conf.

PlantGDB will be represented at the 52nd Annual Maize Genetics Conference, March 18-21, 2010, Riva del Garda, Italy. Check out Poster 151, "Maize Community Annotation Project to Improve Gene Structures" in the 2010_maize_meeting_program.pdf.

New Annotation Workflow at BioExtract

The BioExtract Server has added a powerful new workflow for annotating genomic DNA, based on user-selected transcript and protein databases. The pipeline uses EVM (EVidence Modeler) to evaluate transcript- and ab initio-derived exons, and it outputs a GFF3-formatted file of optimal gene structures. A similar pipeline is available at PlantGDB for use with xGDB genome browsers (see next news item).

New Annotation Pipeline at PlantGDB

The AnnotationPipeDream tool allows users to annotate any genomic region (up to 500 kb) using any combination of transcript and protein datasets. The pipeline uses EVM (EVidence Modeler) to evaluate transcript- and ab initio-derived exons, and it outputs a GFF3-formatted file of optimal gene structures. The pipeline is currently available in the maize genome browser ZmGDB (click "Annotation Pipeline") and will soon be available for all genomes. This pipeline is also available as a customizable workflow in the BioExtract Server (see previous news item).

Community Annotation Tips

The yrGATE tool for gene structure annotation sports new context-sensitive help icons: just click any help icon () for a popup explanation of each function or tool.(Example).

Maize RefGen_v2 genome

The revised pseudomolecule assembly of maize inbred B73 (RefGen_V2) was released on March 5, 2010 by the Arizona Genomics Institute. We are busy running spliced-alignment to maize EST, cDNA, PUT, and related-species protein in anticipation of releasing a new version of ZmGDB (expected May, 2010)

Manihot esculenta (cassava) genome browser

The recently-released Manihot esculenta draft genome consists of 11,243 scaffolds spanning 416Mb. PlantGDB will release a cassava genome browser incorporating EST, cDNA, PUT and related-species protein alignments as well as published gene models (expected May, 2010).