Biomedical, Genetics & Genomics Resources: Core Biomolecular Databases

Biosciences, Genetics & Genomics resource guide for University of Iowa students, residents, fellows & faculty

Biomedical, Genetics & Genomics Resources

Guide content supports the teaching and research goals of multiple departments on campus. Content represents a non-exhaustive selection of essential resources and tools for engaging a wide range of backgrounds and viewpoints.

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Getting Started

The following are some of the more popular resources from the National Center for Biotechnology Information (NCBI).

When using BLAST, click the Help button to access the BLAST tutorials.

Access all of the NCBI Databases
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
Basic Local Alignment Search Tool (BLAST)
Finds regions of local similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families.
Gene
A searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific data. Information includes nomenclature, chromosomal localization, gene products and their attributes (e.g., protein interactions), associated markers, phenotypes, interactions, and links to citations, sequences, variation details, maps, expression reports, homologs, protein domain content, and external databases.
Nucleotide
A collection of nucleotide sequences from several sources, including GenBank, RefSeq, the Third Party Annotation (TPA) database, and PDB. Searching the Nucleotide Database will yield available results from each of its component databases.
Protein
The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.
Structure (Molecular Modeling Database)
The Molecular Modeling Database (MMDB) contains 3D macromolecular structures, including proteins and polynucleotides. MMDB contains over 40,000 structures and is linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxon.

Nucleotide Sequences

Nucleotide
Expressed Sequence Tags
In the process of being merged with the Nucleotide DB, see below.

Protein and Protein Structure

Protein
Structure
Conserved Domain Database
The Conserved Domain Database (CDD) contains protein domain models imported from outside sources, such as Pfam and SMART, and curated at NCBI. CDD contains over 12,000 such models and is linked to other NCBI databases, including protein sequences, bibliog
Protein Data Bank
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.
Protein Clusters
This collection of related protein sequences (clusters) consists of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.