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diArk--the database for eukaryotic genome and transcriptome assemblies in 2014.

Martin Kollmar1, Lotte Kollmar2, Björn Hammesfahr2

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The diArk database provides access to eukaryotic genome and transcriptome assemblies, including novel data not found elsewhere. This resource aids researchers in selecting high-quality datasets for complex biological studies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Eukaryotic genomes are fundamental to understanding life's complexity.
  • Rapid advancements in sequencing technology enable rapid genome and transcriptome assembly.
  • Existing databases may not encompass all available assembled eukaryotic genomic data.

Purpose of the Study:

  • To present diArk, a comprehensive database for accessing assembled eukaryotic genomes and transcriptomes.
  • To provide quality indicators for comparing and selecting genomic datasets.
  • To integrate transcriptome assemblies and enhance data analysis features.

Main Methods:

  • Development of the diArk database (http://www.diark.org).
  • Integration of approximately 6000 genome and transcriptome assemblies for ~2600 eukaryotes.
  • Implementation of quality assessment metrics and user-friendly filtering options.

Main Results:

  • diArk offers access to a substantial collection of eukaryotic genomic and transcriptomic data.
  • A significant portion (22%) of the data in diArk is not available through major public repositories like NCBI/ENA/DDBJ.
  • The database includes quality indicators and enhanced analytical features for user-selected datasets.

Conclusions:

  • diArk serves as a valuable, centralized resource for eukaryotic genomic and transcriptomic data.
  • The database facilitates comparative genomics and transcriptomics research by providing quality metrics and novel data.
  • The updated version enhances accessibility and analytical capabilities for researchers in molecular biology and related fields.