Biological Databases Overview

Study Notes

Nucleotide Sequence Data Base: Stores DNA/nucleotide sequences
Protein Sequences Data Base: Stores protein sequence data
Gene Expression Data Base: Stores and analyzes gene expression data
Clinical Databases: Stores clinical trial data and patient information
Metabolic Pathways Database: Provides information on metabolic pathways and reactions
Structural Databases: Stores 3D structures of proteins, nucleic acids, and other biomolecules

Primary Databases (Archival Databases)
- Includes original data from researchers
- Publicly available for annotation purposes
- Repository of raw and annotated data
- Accessed freely through the internet
- Sequence database:
  - Stores DNA/nucleotide and protein sequences
  - DNA/nucleotide databases:
    - Stores DNA/nucleotide sequence data
    - Share data daily for consistent information across databases
  - Protein database:
    - Stores information on protein sequences
Secondary Databases:
- Contains results from analysis of primary database entries
- Manually curated or automatically generated
- Derived from the analysis of primary data
- May utilize data from numerous sources
- Information includes conserved sequences, signature sequences, active site residues of protein families
Curated Databases:
- Maintained by curators who select only the highest quality data
- Emphasize the high quality of data over quantity
Composite Databases:
- Combine different primary databases
- Efficiently query and search multiple sources
- Non-redundancy is maintained by filtering data from various primary sources
- Merge diverse primary resources, reducing the need to search multiple databases

NCBI (National Center for Biotechnology Information): A comprehensive resource for biological information, including GenBank, PubMed, and BLAST.
EMBL (European Molecular Biology Laboratory): A nucleotide sequence database similar to GenBank.
UniProt (Universal Protein Resource): A database of protein sequences and functional information.
PDB (Protein Data Bank): A repository of 3D structural data for proteins and nucleic acids.
PlantPepDB (Plant Protein Database): A database focusing on plant protein sequences and their associated information.