Abstract
BackgroundThe Ashbya Genome Database (AGD) 3.0 is an innovative cross-species genome and transcriptome browser based on release 40 of the Ensembl developer environment.DescriptionAGD 3.0 provides information on 4726 protein-encoding loci and 293 non-coding RNA genes present in the genome of the filamentous fungus Ashbya gossypii. A synteny viewer depicts the chromosomal location and orientation of orthologous genes in the budding yeast Saccharomyces cerevisiae. Genome-wide expression profiling data obtained with high-density oligonucleotide microarrays (GeneChips) are available for nearly all currently annotated protein-coding loci in A. gossypii and S. cerevisiae.ConclusionAGD 3.0 hence provides yeast- and genome biologists with comprehensive report pages including reliable DNA annotation, Gene Ontology terms associated with S. cerevisiae orthologues and RNA expression data as well as numerous links to external sources of information. The database is accessible at .
Highlights
The Ashbya Genome Database (AGD) 3.0 is an innovative cross-species genome and transcriptome browser based on release 40 of the Ensembl developer environment.Description: AGD 3.0 provides information on 4726 protein-encoding loci and 293 non-coding RNA genes present in the genome of the filamentous fungus Ashbya gossypii
This paper reports the release of Ashbya Genome Database 3.0, an innovative cross-species genome and transcriptome browser based on the Ensembl environment
In the DetailedView section, pop-up menus can be used to display different features: genes, homologous regions from other fungal species mapped by BLASTZ and, notably, the positions of the target sequences covered by oligonucleotide probes on Ashbya and yeast GeneChips
Summary
AGD 3.0 is a useful and innovative database for researchers in the yeast and genome evolution fields. The gene annotation data is steadily verified and improved and it is complemented with high-density oligonucleotide microarray expression data. This approach marks out AGD 3.0 as the first database that enables users to view a comprehensive report page including information on gene DNA annotation and RNA expression across conserved fungal species. AG developed the database, RR contributed microarray expression data, PD participated in array data production, FSD participated in genome annotation and GeneChip development, PP lead the genome annotation project, MP a http://www.biomedcentral.com/1471-2164/8/9 b. Panels b and c show a bar diagram of normalized array expression signals obtained with germinating Ashbya spores and hyphae growing on rich medium compared to data obtained for the budding yeast orthologs expressed on various growth and sporulation media as indicated.
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