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This page is a list of useful tools and databases for biologists. Major Updates 26/01/23.

Published

January 23, 2026

✎505 ♥

I mainly use R for all analysis.

1 Wet Lab Tools/Databases

1.1 General

ATCC: Product provider.

1.2 Biochemistry Assays

Addgene: A database for plasmids and vectors.
NEB Restriction Endonucleases/Buffer Chart: A reference table for NEB endonucleases.
TALEN Designer: A TALEN vector designer.
NCBI Primer Blast: Primer designing tool.
AAT Bioquest: Restriction Enzymes Cut Sizes Reference Table.
Vitascientific.com: Melting Temperature (Tm) Calculation.
SignalP: Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms.
Genetic Pertubation Platform (GPP)/RNAi Platform: A collection of webtools for RNAi - functional investigations of the mammalian genome that can reveal how genetic alterations lead to changes in phenotype, by Broad Institute.
CHOPCHOP: A web tool for selecting target sites for CRISPR/Cas9 etc.-directed mutagenesis.
OmniGuide RNA Design Tool: A web tool to design high-performance CRISPR guide RNAs by GenScript.

1.3 Microscopy/Imaging

CellProfiler: Open-source image processing software.

1.4 Cell Culture

Useful Numbers for Cell Culture: The ThermoFisher cell culture guide.

1.5 Model Organisms

The Jackson Laboratory: A database for mouse models.
TAIR: An Arabidopsis information database.

2 Bioinformatics Tools/Databases

2.1 General

BioConductor: A powerful R package for bioinformatics analysis.

2.2 Databases

NIH National Center for Biotechnology Information (NCBI): The ultimate biology database.
- NCBI dbSNP: A database of human single nucleotide variations, microsatellites, and small-scale indels.
EMBL’s European Bioinformatics Instituten (EMBL-EBI): Unleashing the potential of big data in biology.

2.2.1 Human

GeneCards: An integrative database on all annotated and predicted human genes by the Weizmann Institute of Science.
The Human Protein Atlas: An open access resource for human proteins.

2.2.1.1 Pharmacogenomics

PharmGKB/ClinPGx: A comprehensive clinical pharmacogenomics (PGx) resource database.
Pharmacogene Variation Consortium (PharmVar): A database for drug-related genes.
Clinical Pharmacogenetics Implementation Consortium (CPIC): A database for drug-related genes.

2.2.2 Microbiology

CARD/The Comprehensive Antibiotic Resistance Database: A database for ARGs/ARBs.
ViralZone: A database for information on viruses (descriptions, images, and classifications) maintained by the Swiss-Prot group and SIB.
The Global Initiative on Sharing All Influenza Data (GISAID): A database for recent variants of hCoV-19, Dengue, Influenza, Mpox and RSV.

2.3 Sequence Alignment/Search

NCBI BLAST/Basic Local Alignment Search Tool: comparing primary biological information like nucleotide and amino acid sequences.

2.4 Protein Structural Biology

CSB PDB/Protein Data Bank: A database for protein structures.
AlphaFold: A database/tool for protein structures predicted by AlphaFold.
- AlphaFold Server: A web-service that generate biomolecular structure predictions.
UniProt: A database for protein sequence and functional information.
UCSF Chimera: A tool for protein 3D structure analysis.
SWISS-MODEL: A fully automated protein structure homology-modelling server.
FoldSeek: A web tool for fast and sensitive comparisons of large protein structure sets.

2.5 Phylogenetics

phyloseq: R package for microbiome analysis.
TimeTree: The Timescale of Life: A tool for phylogenetic analysis (for fun).

2.6 Functional Analysis/Gene Annotation

Gene Ontology (GO): A bioinformatics initiative to unify the representation of gene and gene product attributes across all species. Basically, a gene functional annotation database.
- GO terms/description full list (all organisms)
- AmiGO2: The official tool to search and browse the GO database.
- QuickGO: The EMBL database for GO terms.
- ontologyIndex: An R package to navigate through .obo files.
eggNOG: The EMBL database of orthology relationships, functional annotation, and gene evolutionary histories.
- eggNOG-mapper: Using the eggNOG database to map gene functions.
PolyPhen-2: A tool for predicting possible impact of AAS on the structure and function of a human protein.

2.7 Next-Generation Sequencing (NGS) Analysis

INSaFLU-TELEVIR: A web-based tool to deal with NGS data for metagenomics virus detection and routine genomic surveillance.
NextStrain: An open-source project to harness the scientific and public health potential of pathogen genome data.
DADA2: An analysis tool for Illumina Miseq data.

3 Misc.

3.1 Data Visualization

GraphPad Prism: A graphing and statistics software for scientists.
ggplot2: We have GraphPad Prism at home!
BioRender: A tool to make scientific graphs.
SwissBioPics: An interactive library of cell images for the visualization of subcellular location data.
RNArtist: A tool for RNA 2D structure visualization.
ViralVar: A platform for the visualization of viral lineages and mutations.

3.2 Wet Lab Simulation

SnapGene: A desktop software to simulate DNA cloning and genetic engineering experiments.
Benchling: A cloud-based platform similar to SnapGene.

3.3 Forums

Biostars Forum: A bioinformatics forum.
r/bioinformatics: The reddit bioinformatics forum.
r/labrats: The reddit wet lab forum.

3.4 Blogs/Tips/Tutorials

3.4.1 Uncategorized

Virology Blog: A blog about viruses and viral diseases.

3.4.2 Bioinformatics

3.4.2.1 Protein Structural Biology

PyMOL Advanced Scripting Tutorial

3.4.3 Microscopy/Imaging

A Beginner’s Guide to Creating Fluorescence Bioimages for Scientific Publication

3.4.5 Sequencing

3.4.6 CRISPR

3.5 Misc. Databases & Tools

Kudos ♥

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