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Biological Databases

The document outlines various nucleotide and protein sequence databases, including GenBank, EMBL-ENA, and DDBJ for nucleotide sequences, and UniProt and InterPro for protein sequences. It also highlights databases for genome annotation, protein structure, pathway information, gene expression, and clinical variants, such as Ensembl, PDB, KEGG, GEO, and ClinVar. These resources are essential for researchers in genomics and bioinformatics, providing access to a wealth of biological data.

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2 views2 pages

Biological Databases

The document outlines various nucleotide and protein sequence databases, including GenBank, EMBL-ENA, and DDBJ for nucleotide sequences, and UniProt and InterPro for protein sequences. It also highlights databases for genome annotation, protein structure, pathway information, gene expression, and clinical variants, such as Ensembl, PDB, KEGG, GEO, and ClinVar. These resources are essential for researchers in genomics and bioinformatics, providing access to a wealth of biological data.

Uploaded by

melsayedf.2006
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© All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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A.

Nucleotide (DNA/RNA) Sequence Databases

1. GenBank (NCBI)

A comprehensive public database containing DNA and RNA sequences submitted by


researchers worldwide. It is one of the largest repositories for raw nucleotide data and is widely
used as a global reference.

2. EMBL-ENA (European Nucleotide Archive)

Europe’s primary archive for nucleotide sequences. It stores raw sequencing reads, assembled
genomes, and annotated sequence data, ensuring open access and long-term preservation.

3. DDBJ (DNA Data Bank of Japan)

Japan’s national nucleotide sequence database. It collaborates closely with GenBank and ENA
to synchronize global DNA sequence data as part of the INSDC.

B. Genome Browser / Genome Annotation Database

4. Ensembl

A powerful genome browser offering annotated genomes for vertebrates and other eukaryotes.
It provides gene structures, variants, comparative genomics, and evolutionary analyses.

C. Protein Sequence & Functional Databases

5. UniProt (Universal Protein Resource)

The gold-standard database for protein sequence and functional information. It provides highly
curated protein entries with details on structure, function, domains, and biological roles.

6. InterPro

A protein family and domain database that integrates predictive models from multiple member
databases. It classifies proteins into families and identifies domains, motifs, and functional
sites.

D. Protein Structure Database

7. PDB (Protein Data Bank)

The world’s central repository for 3D structural data of proteins, nucleic acids, and complexes.
Structures are determined through X-ray crystallography, NMR spectroscopy, or cryo-EM.

Mohammad Elsayed
E. Pathway, Systems Biology, & Functional Databases

8. KEGG (Kyoto Encyclopaedia of Genes and Genomes)

A database integrating genomic, chemical, and pathway information. It maps metabolic


pathways, signalling pathways, and disease networks to help understand biological systems.

F. Gene Expression / Functional Genomics Database

9. GEO (Gene Expression Omnibus)

A public repository for high-throughput gene expression data, including microarray and RNA-
seq experiments. It allows researchers to access, compare, and analyse gene expression
profiles.

G. Clinical Variant Database

10. ClinVar

A freely accessible database that connects human genetic variants to their clinical
significance. It helps interpret whether variants are benign, pathogenic, or uncertain in relation
to disease.

Mohammad Elsayed

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