Bioinformatics Databases
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Questions and Answers

What is the primary purpose of biological databases?

To understand and explain biological phenomena, as well as facilitate the fight against diseases and develop medications.

What is a common challenge in managing biological databases?

Ensuring the consistency of information across different databases.

What is the primary function of a database?

To store, search, and retrieve vast amounts of information.

What was one of the first biological sequence databases?

<p>The book 'Atlas of Protein Sequences and Structures' by Margaret Dayhoff and colleagues.</p> Signup and view all the answers

What is the purpose of accession numbers in biological databases?

<p>To cross-reference and link related knowledge across different databases.</p> Signup and view all the answers

What is the significance of central, shareable resources in biological databases?

<p>They enable the assembly and analysis of biological data.</p> Signup and view all the answers

What is the relationship between primary and secondary databases?

<p>Primary databases store raw biological data, while secondary databases store derived data and annotations.</p> Signup and view all the answers

What is the role of bioinformatics tools in biological databases?

<p>To analyze and interpret biological data.</p> Signup and view all the answers

What is a composite database?

<p>A database that combines data from multiple sources.</p> Signup and view all the answers

What is the significance of data formatting in biological databases?

<p>It enables the efficient storage and retrieval of biological data.</p> Signup and view all the answers

Study Notes

Biological Databases

  • Types of biological databases:
    • Nucleic acid databases (e.g. GenBank, EMBL, DDBJ)
    • Protein databases (primary: PDB, MMDB; secondary: Swiss-Prot, Pfam)
    • Whole genome databases (e.g. TIGR)
    • Metabolic pathway databases (e.g. EMP, KEGG)
    • Organism-specific databases (e.g. Ebola, S. aureus, A. thaliana, mouse genome)

Important Bioinformatics Databases

  • GenBank: nucleotide sequences
  • Ensembl: human/mouse genome and others
  • PubMed: literature references
  • SWISS-PROT: protein sequences
  • InterPro: protein domains
  • OMIM: genetic diseases
  • PDB: protein structures
  • KEGG: metabolic pathways

Why Biological Databases?

  • Need for storing and communicating large datasets
  • Make biological data available to scientists in computer-readable form
  • Support large-scale analysis efforts
  • Make data access easy and updated
  • Link knowledge obtained from various fields of biology and medicine

Characteristics of Biological Databases

  • Depend on the nature of information stored (sequences, images, etc.)
  • Depend on the manner of storage (flat files, relational databases, etc.)

Importance of Biological Databases

  • Assist scientists in understanding biological phenomena
  • Facilitate the fight against diseases
  • Assist in the development of medications
  • Help in discovering basic relationships amongst species in the history of life

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Test your knowledge of bioinformatics databases, including nucleic acid databases like GenBank and EMBL, protein databases like PDB, and whole genome databases like TIGR.

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