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EuMicrobedbLite: A lightweight genomic resource and analytic platform for draft oomycete genomes

Arijit Panda, Diya Sen, Arup Ghosh, Akash Gupta, Malar C Mathu, Gyan Prakash Mishra, Deeksha Singh, Wenwu Ye, Brett M. Tyler, Sucheta Tripathy
doi: https://doi.org/10.1101/084483
Arijit Panda
1Computational Genomics lab, 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.
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Diya Sen
1Computational Genomics lab, 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.
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Arup Ghosh
1Computational Genomics lab, 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.
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Akash Gupta
1Computational Genomics lab, 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.
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Malar C Mathu
1Computational Genomics lab, 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.
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Gyan Prakash Mishra
1Computational Genomics lab, 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.
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Deeksha Singh
1Computational Genomics lab, 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.
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Wenwu Ye
2Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-7303.
3Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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Brett M. Tyler
2Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-7303.
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Sucheta Tripathy
1Computational Genomics lab, 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.
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Abstract

We have developed EuMicrobedbLite – A light weight 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, the GUS schema has been greatly simplified with removal of many obsolete modules and redesign of others to incorporate contemporary data. Several dependencies such as perl object layers used for data loading in VMD have been replaced with independent light weight scripts. EumicrobedbLite now runs on a powerful annotation engine developed at our lab called “Genome Annotator Lite”. Currently this database has 26 publicly available genomes and 10 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 twelve oomycete organisms that form 2974 clusters. Synteny viewing is enabled by 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 six months to ensure quality. The database resource is available at www.eumicrobedb.org.

Abbreviations
eumicrobedblite
GUS, VMD, GFF, GO, KEGG, KAAS, KOG, TMHMM
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Posted October 31, 2016.
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EuMicrobedbLite: A lightweight genomic resource and analytic platform for draft oomycete genomes
Arijit Panda, Diya Sen, Arup Ghosh, Akash Gupta, Malar C Mathu, Gyan Prakash Mishra, Deeksha Singh, Wenwu Ye, Brett M. Tyler, Sucheta Tripathy
bioRxiv 084483; doi: https://doi.org/10.1101/084483
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EuMicrobedbLite: A lightweight genomic resource and analytic platform for draft oomycete genomes
Arijit Panda, Diya Sen, Arup Ghosh, Akash Gupta, Malar C Mathu, Gyan Prakash Mishra, Deeksha Singh, Wenwu Ye, Brett M. Tyler, Sucheta Tripathy
bioRxiv 084483; doi: https://doi.org/10.1101/084483

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