title: EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes.
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.
authors: Computational 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.
authors: Arijit
authors: A
authors: Panda
authors: Computational 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.
authors: Diya
authors: D
authors: Sen
authors: Computational 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.
authors: Arup
authors: A
authors: Ghosh
authors: Computational 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.
authors: Akash
authors: A
authors: Gupta
authors: Computational 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.
authors: Mathu Malar
authors: MM
authors: C
authors: Computational 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.
authors: Gyan
authors: G
authors: Prakash Mishra
authors: Computational 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.
authors: Deeksha
authors: D
authors: Singh
authors: Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331-7303, USA.|Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China.
authors: Wenwu
authors: W
authors: Ye
authors: Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331-7303, USA.
authors: Brett M
authors: BM
authors: Tyler
authors: Computational 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.
authors: Sucheta
authors: 0000-0003-0611-8088
authors: S
authors: Tripathy
mesh_terms: D030541:Databases, Genetic; D016678:Genome; D058977:Molecular Sequence Annotation; D009868:Oomycetes / Q000235:genetics*; D012984:Software; D026801:Synteny / Q000235:genetics; D014584:User-Computer Interface
keywords: comparative genomics; database; genome browser; oomycetes; orthologous genes; toolkit