NAR Database update 2020

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DNAproDB

DNA–protein complex structure analysis
Paper
Document

  • Update
    • Structure processing upgrades
    • Data update
    • Database and web interface
      • Search
      • Report
      • Integration with Nucleic Acid Database
  • Discussion and conclusion
    • case study

EnhancerAtlas

Enhancers in nine species
Paper
Document

  • Materals and methods
    • Data sources
    • Data processing for individual dataset/track
    • Generation of consensus track
    • Enhancer-gene interactions
    • Implenentation of database
  • Results
    • statistics
    • Database search
    • Enhancer browser

GWAS Central

GWAS datasets
Paper
Document

  • Materials and methods
    • Data collection and curation
    • Ontology mapping
    • Database design
  • Results
    • GWAS data searching
    • Data visualization
  • Discussion

MatrisomeDB

Extracellular matrix components
Paper
Document

  • Database infrastructure
    • Data sets included
    • Mass spectrometry data search and processing
  • Database features and functionalities
    • MatrisomeDB query
    • Hierarchically-clustered protein distribution heatmap
    • Peptide converage map
  • Results
    • Experimental coverage of the in-silico predicted matrisome
    • Building an ECM atlas
  • Future directions
    • Future data extension
    • Extension to include studies from other model organisms
    • Extracting quantitative data from label-free and label-based proteomics studies

MIBiG

Biosynthetic Gene Clusters of Known Function
Paper
Document: No

  • Methods and implementation
    • Manual curation of entries
    • Data quality improvements
    • The new database architecture
  • Results and discussion
    • Data overview
      • BGC diversity
      • Annotation completeness
    • A new online repository

MirGeneDB

Animal miRNA complements
Paper
Document

  • Expansion of MirGeneDB
  • Quality of MirGeneDB annotations
  • Improved web interface of MirGeneDB
  • MiRNA nomenclature
  • Functional classfication of MiRNA-seeds
  • Future developments

MSDB

Microsatellites from all sequenced genomes
Paper
Document

  • Materials and methods
    • Data sources
    • Identification of repeats
    • Database design
    • Web interface
  • Database overview and functionality
    • Dashbord view
    • Species selection
    • Modal view
    • Tabel view
    • Data download
    • Help page
  • Discussion
    • Case study 1: length preference of AGAT repeats
    • Case study 2: enrichment of AGC repeats in ruminants

Ohnologs

Vertebrate ohnologs
Paper
Document

  • Results
    • Data collection and processing
    • Navigating teh OHNOLOGS database
    • Summary of the contents of the OHNOLOGS database

PolyASite

RNA polyadenylation sites
Paper
Document

  • Materials and methods
    • Protocal-spefici pre-processing of reads
    • Uniform analysis of putative poly(A) sites in individual samples
    • Clustering of closely spaced sites
    • Annotation and quantification of pply(A) sites
  • Results
    • Website roadmap

WALTZ-DB

Amyloidogenic peptide sequences
Paper
Document

  • Expanded content and feature improvements
    • New peptide entries and database statistics
    • WALTZ-DB 2.0 novel features
  • Materials and methods
    • Peptide synthesis
    • Determination of amyloid fibril properties
    • Structural models and energy calculations
  • Links to other databases