Guides: Bioinformatics: Bioinformatics Tools and databases

Selecting a database or tool

Nucleic Acids Research 2024 Database Issue

Nucleic Acids Research's annual Database Issue categorizes many of the publicly available online databases related to molecular biology and bioinformatics as well as recent updates to databases

Nucleic Acids Research 2024 Web Server Issue

Nucleic Acids Research's annual issues dedicated to web-based software resources for analysis and visualization of molecular biology data.

MolBio Information Service

Created by the University of Pittsburgh Health Sciences Library System. Find molecular databases and software tools using a combined search of the HSLS Online Bioinformatics Resource Collection (OBRC), Nucleic Acids Research Database/Web Server Issues, and a filtered PubMed search. You can also search for protocols, videos, or preprints.

Genes, nucleotides and genomes

ArrayExpress
ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community.
BLAST (Basic Local Alignment Search Tool)
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
DNA Databank of Japan
DDBJ Center collects nucleotide sequence data as a member of INSDC (International Nucleotide Sequence Database Collaboration) and provides freely available nucleotide sequence data and supercomputer system, to support research activities in life science.
European Nucleotide Archive (EMBL-EBI)
The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation.
GenePattern
A powerful scientific workflow system that provides access to hundreds of genomic analysis tools. Designed to enable researchers to develop, capture, and reproduce genomic analysis methodologies.
Genome
This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations.
IHEC
The International Human Epigenome Consortium (IHEC) makes available comprehensive sets of reference epigenomes relevant to health and disease.
Joint Genome Institute Data & Tools
A suite of databases and tools to conducting genome and metagenome studies.
Nucleotide
The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
UCSC Genome Browser
Tool that allows you to interactively visualize genomic data of various model organisms.
VISTA
VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences.

Gene (NCBI)
Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
GEO DataSets (NCBI)
This database stores curated gene expression DataSets, as well as original Series and Platform records in the Gene Expression Omnibus (GEO) repository. Enter search terms to locate experiments of interest. DataSet records contain additional resources including cluster tools and differential expression queries.

Proteins and proteomes

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.
Protein Data Bank
Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.
Reactome
An open-source, open access, manually curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome analysis, modeling, systems biology and education.
UniProt
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

Conserved Domain Database

This is a resource for the annotation of functional units in proteins. Its collection of domain models includes a set curated by NCBI, which utilizes 3D structure to provide insights into sequence/structure/function relationships.

Identical Protein Groups

This resource contains a single entry for each protein translation found in several sources at NCBI, including annotated coding regions in GenBank and RefSeq, as well as records from SwissProt and PDB. This resource allows investigators to obtain more targeted search results and quickly identify a protein of interest.

Protein Family Models

This database is a collection of models representing homologous proteins with a common function. It includes conserved domain architecture, hidden Markov models and BlastRules.