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Updated: Mar 13, 2026
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Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Published on: July 28, 2017
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EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes
Arijit Panda1, Diya Sen1, Arup Ghosh1
1Computational Genomics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research -Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, India.
Molecular Plant Pathology
|October 28, 2016
Summary
EumicrobeDBLite offers a streamlined platform for oomycete genome analysis, featuring updated comparative genomics and enhanced user tools. This resource provides valuable insights into oomycete biology and evolution.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Oomycete research requires comprehensive genome resources.
- Previous databases like VBI Microbial Database (VMD) had limitations.
- Need for an updated, user-friendly platform for oomycete sequence analysis.
Purpose of the Study:
- To develop EumicrobeDBLite, a lightweight, comprehensive genome resource and analysis platform for oomycetes.
- To improve upon the VBI Microbial Database (VMD) with a simplified schema and modern architecture.
- To provide enhanced comparative genomics and user-friendly browsing capabilities.
Main Methods:
- Redesigned Genome Unified Schema (GUS) by removing obsolete modules.
- Replaced Perl object layers with independent lightweight scripts.
- Integrated a new annotation engine, 'Genome Annotator Lite', and the Genome Synteny Viewer (GSV) tool.
Main Results:
- EumicrobeDBLite now hosts 26 oomycete genomes and 10 EST datasets.
- Identified 44,777 core conserved proteins forming 2974 clusters across 12 oomycete species.
- Implemented dynamic comparative genomics tracks, GFF file upload, and EMBOSS toolkit integration.
Conclusions:
- EumicrobeDBLite provides a significantly enhanced and accessible resource for oomycete genomics.
- The platform facilitates advanced comparative genomics, ortholog identification, and pathway analysis.
- Regular annotation updates ensure the database remains a high-quality, up-to-date research tool.
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