ArticleMolecular plant pathology2018
EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes.
Article in Molecular plant pathology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- Comparative Genome Analysis Across 128Frontiers in microbiology · 2022Article
- Conserved Subgroups of the Plant-Specific RWP-RK Transcription Factor Family Are Present in Oomycete Pathogens.Frontiers in microbiology · 2020Article
- Genome/transcriptome collection of plethora of economically important, previously unexplored organisms from India and abroad.Data in brief · 2019Article
- Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution.PLoS pathogens · 2019Article
- Oomycete Gene Table: an online database for comparative genomic analyses of the oomycete microorganisms.Database : the journal of biological databases and curation · 2019Article
- Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB).Genome biology and evolution · 2019Article
- Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.Genome biology and evolution · 2018Article
- Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts.BMC genomics · 2018Article
- Large sub-clonal variation in Phytophthora infestans from recent severe late blight epidemics in India.Scientific reports · 2018Article
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Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed EumicrobeDBLite-a lightweight comprehensive genome resource and sequence analysis platform for oomycete organisms. EumicrobeDBLite is a successor of the VBI Microbial Database (VMD) that was built using the Genome Unified Schema (GUS). In this version, GUS has been greatly simplified with the removal of many obsolete modules and the redesign of others to incorporate contemporary data. Several dependences, such as perl object layers used for data loading in VMD, have been replaced with independent lightweight scripts. EumicrobeDBLite now runs on a powerful annotation engine developed at our laboratory, called 'Genome Annotator Lite'. Currently, this database has 26 publicly available genomes and 10 expressed sequence tag (EST) datasets of oomycete organisms. The browser page has dynamic tracks presenting comparative genomics analyses, coding and non-coding data, tRNA genes, repeats and EST alignments. In addition, we have defined 44 777 core conserved proteins from 12 oomycete organisms which form 2974 clusters. Synteny viewing is enabled by the incorporation of the Genome Synteny Viewer (GSV) tool. The user interface has undergone major changes for ease of browsing. Queryable comparative genomics information, conserved orthologous genes and pathways are among the new key features updated in this database. The browser has been upgraded to enable user upload of GFF files for quick view of genome annotation comparisons. The toolkit page integrates the EMBOSS package and has a gene prediction tool. Annotations for the organisms are updated once every 6 months to ensure quality. The database resource is available at www.eumicrobedb.org.
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