DATABASES
Nucleotide and Protein Sequences
- Genbank - Explore Genbank, the nucleotide sequence database at NCBI.
- ENA - European Nucleotide Archive at EMBL-EBI, providing comprehensive nucleotide sequence data.
- DDBJ - DNA Data Bank of Japan, a repository for DNA sequence data.
- Protein database at NCBI - Access the protein database for protein sequence information.
- UniProt - Explore UniProt, a resource providing protein sequence and functional information.
Genome Downloads
- NCBI - National Center for Biotechnology Information (NCBI) provides access to genomic data for research and analysis.
- Ensembl - Ensembl offers a comprehensive genome database with tools for exploring and analyzing genomic data.
Genome Browsers
- Genome Data Viewer (NCBI) - Explore genomic data using the Genome Data Viewer by NCBI.
- Ensembl - Access the Ensembl genome browser for comprehensive genomic information.
- UCSC genome browser - Navigate and analyze genomic sequences using the UCSC Genome Browser.
Gene Databases
- Gene - Explore the gene database at NCBI for comprehensive gene information.
- UniGene - Access the UniGene database at NCBI, focusing on transcript information.
- SOURCE - Explore SOURCE, a gene database for detailed gene-related data.
- GeneAtlas - GeneAtlas is a comprehensive gene database providing detailed information.
- GeneCards - GeneCards is a human gene database with a wealth of gene-related information.
- OMIM - OMIM is an Online Catalog of Human Genes and Genetic Disorders, offering valuable genetic insights.
- AmiGo - AmiGo is a gene ontology database providing comprehensive gene-related information.
- HGNC - HGNC (HUGO Gene Nomenclature Committee) is a reliable source for gene nomenclature information.
- GENCODE - GENCODE is a human and mouse gene annotation database offering detailed gene annotations.
- Harmonizome - Harmonizome provides integrated knowledge about genes and proteins for comprehensive insights.
Gene Mutations and Variations
- dbSNP - a database of single nucleotide polymorphisms (SNPs) and small-scale insertions/deletions, microsatellites, and non-polymorphic variants
- ClinVar - an archive of reports of the relationships among human variations and phenotypes
- MutDB - a database for assessing the impact of genetic variants
- HGMD - The Human Gene Mutation Database
- GWAS Central - a centralized compilation of summary level findings from genetic association studies
- DGV - a curated catalogue of human genomic structural variation
Gene Expression
- Expression Atlas - gene and protein expression across species and biological conditions
- GEO - Gene Expression Omnibus
- ArrayExpress - data from high-throughput functional genomics experiments
- GTEx - The Genotype-Tissue Expression Project
- Bgee - gene expression patterns in multiple animal species
- OmicsDI - The Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics).
Epigenetics
- Roadmap Epigenomics Project
- VizHub - Roadmap Epigenomics Visualization Hub
- DeepBlue - Epigenomic Data Server
- PubMeth - annotated and reviewed database of methylation in cancer
Gene Regulatory Elements
- EPD - Eukaryotic Promoter Database
- JASPAR - transcription factor binding profile database
- ENCODE - Encyclopedia of DNA Elements
- TRRUST - a manually curated database of human transcriptional regulatory network
- FANTOM5 promoterome
- Cistrome - integrative analysis pipelines to better mine the hidden biological insights from publicly available high throughput data
- ChIP-Atlas - integrative and comprehensive database for visualizing and making use of public ChIP-seq data
- GTRD - Gene Transcription Regulation Database
- ChIPBase - a database for studying the transcription factor binding sites and motifs, and decoding the transcriptional regulatory networks of lncRNAs, miRNAs, other ncRNAs and protein-coding genes from ChIP-seq data
Non-Coding RNA Databases and Tools
- miRBase - a searchable database of published miRNA sequences and annotation
- miRTarBase - the experimentally validated microRNA-target interactions database
- miRDB - online database for miRNA target prediction and functional annotations
- TargetScan - prediction of microRNA targets
- RNA22 - microRNA target detection
- DIANA Tools - databases of experimentally verified miRNA targets and prediction tools
- NONCODE - An integrated knowledge database dedicated to ncRNAs, especially lncRNAs
Protein Function and Regulation
Enzymes
- BRENDA - the comprehensive enzyme information system
- MetaCyc - Metabolic Encyclopedia (enzymes, metabolites and metabolic pathways)
- IntEnz - Integrated Relational Enzyme Database
- ExplorEnz - the enzyme database
- KEGG ENZYME Database
- MEROPS - an information resource for peptidases
- REBASE - The Restriction Enzyme Database
Signaling pathways
- KEGG PATHWAY Database
- NetPath - manually curated resource of signal transduction pathways in humans
- Reactome - a signaling pathway database
- WikiPathways - a database of biological pathways
Protein phosphorylation
- Phospho.ELM - phosphorylation site database
- PHOSIDA - phosphorylation site database
- dbPAF - database of phospho-sites in animals and fungi
- PhosphoNET - human phosphosite knowledgebase
- DEPOD - the human DEPhOsphorylation database
Protein-protein interactions
- IntAct - a protein interaction database at EBI
- BioGRID - a repository for interaction datasets
- STRING - known and predicted protein-protein interactions
Protein abundance and localization
- The Human Protein Atlas - an effort to map all the human proteins in cells, tissues and organs using integration of various omics technologies
- PaxDb - Protein Abundance Database
Structure Databases
- PDB - Protein Data Bank
- CATH - a classification of protein structures from the Protein Data Bank
- Protein Model Portal (PMP) - access to computed models and interactive services for model building
- RNA Bricks - a database of RNA 3D structure motifs and their contacts
- COSMIC-3D - a platform for understanding cancer mutations in the context of 3D protein structure
Small Molecules
- Pubchem - an open chemistry database at the National Institutes of Health
- ChEBI - Chemical Entities of Biological Interest (ChEBI), a freely available dictionary of molecular entities focused on "small" chemical compounds
- DRUGBANK - a pharmaceutical knowledge base
- HMDB - The Human Metabolome Database
Cancer-related Resources
- GDC Data Portal - platform that allows to search and download cancer data for analysis (from the TCGA and other projects)
- COSMIC - the Catalogue Of Somatic Mutations In Cancer
- cBioportal - visualization, analysis and download of large-scale cancer genomics data sets
- Oncoscape - patterns and relationships between clinical and molecular factors
- GEPIA - interactive web server for analyzing the RNA-seq data of tumors and normal samples from the TCGA and the GTEx projects
- canSAR - an integrated knowledge-base that brings together multidisciplinary data across biology, chemistry, pharmacology, structural biology, cellular networks and clinical annotations, and applies machine learning approaches to provide drug-discovery useful predictions
- CCLE - Cancer Cell Line Encyclopedia
- DepMap - Cancer Dependency Map
- GDSC - Genomics of Drug Sensitivity in Cancer
Species-specific Resources
- MGI - Mouse Genome Informatics
- IMPC - International Mouse Phenotyping Consortium
- RGD - The Rat Genome Database
- ZFIN - The Zebrafish Information Network
- XenBase - resources related to biology of X. laevis and X. tropicalis
- FlyBase - resources related to biology of D. melanogaster and other Drosophilidae
- WormBase - resources related to biology of C. elegans and related nematodes
- PomBase - a comprehensive database for the fission yeast Schizosaccharomyces pombe
- SGD - Saccharomyces Genome Database (SGD), comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae
- TAIR - The Arabidopsis Information Resource
Other Resources
- Genetic Codes NCBI webpage - Explore genetic codes on the NCBI website for a better understanding of nucleotide translation.
- Kazusa codon usage database - Access the Kazusa Codon Usage Database to study codon usage patterns in various organisms.
- Codon usage table database at HIVE - Find codon usage tables and related information at the HIVE Codon Usage Table Database.
- NEB list of compatible cohesive ends - New England Biolabs provides a list of compatible cohesive ends for DNA cloning.
- Genomics Data File Formats - Learn about various genomics data file formats on the UCSC Genome Browser FAQ.
ONLINE TOOLS
Sequence Alignment
- Alignment of Sequences with Nucleotide BLAST at NCBI - Perform sequence alignment using the Nucleotide BLAST tool at NCBI.
- Needleman-Wunsch Global Alignment at NCBI - Explore global sequence alignment using the Needleman-Wunsch algorithm at NCBI.
- Clustal Omega at EMBL-EBI - Utilize Clustal Omega for multiple sequence alignment at EMBL-EBI.
- ClustalW at Kyoto University Bioinformatics Center - Perform sequence alignment using ClustalW at Kyoto University Bioinformatics Center.
- MAFFT at EMBL-EBI (Multiple Alignment using Fast Fourier Transform) - Use MAFFT for multiple sequence alignment based on the Fast Fourier Transform algorithm at EMBL-EBI.
- MAFFT at CBRC - Access MAFFT for multiple sequence alignment at the CBRC.
- EMBOSS Water - Smith-Waterman algorithm-based local alignment of sequences - Utilize EMBOSS Water for local sequence alignment using the Smith-Waterman algorithm.
PCR primer design
- Primer-BLAST at NCBI
- Primer3 - online primer design software
- Primer3Plus - online primer design software
- genefisher2 - online primer design software
- OligoCalc - oligonucleotide properties calculator
- OligoAnalyzer (IDT, requires registration)
- Multiple Primer Analyzer at Thermo Fisher Scientific
- OLIGO ANALYSIS TOOL at Eurofins
- PrimerBank - pre-designed PCR primers for gene expression detection and quantification
siRNA/shRNA Design
- Gene Link shRNA design tool
- DSIR - Designer of Small Interfering RNA
- BLOCK-iT RNAi Designer
- E-RNAi at DKFZ
CRISPR Design
- CRISPRdirect - Explore CRISPRdirect for CRISPR guide RNA design and off-target prediction.
- CRISPR Design at MIT - Use the CRISPR Design tool from MIT for designing CRISPR guide RNAs.
- CRISPR gRNA Design tool by DNA2.0 company - Design CRISPR guide RNAs with the CRISPR gRNA Design tool provided by DNA2.0 company.
- Off-Spotter - Explore Off-Spotter for predicting potential off-targets in CRISPR experiments.
- Cas-OFFinder - Use Cas-OFFinder for finding potential off-target sites for CRISPR guide RNAs.
- E-CRISP - Explore E-CRISP for CRISPR guide RNA design and evaluation.
- CRISPOR - Utilize CRISPOR for efficient CRISPR guide RNA design and evaluation.
RNA Secondary Structure Prediction
- RNAfold - A web server for predicting the secondary structure of single-stranded RNA sequences.
- RNAstructure - Tools for the prediction and analysis of RNA secondary structure and thermodynamics.
- mfold - A web server for predicting the secondary structure of RNA sequences through thermodynamic calculations.
- Context Fold - A tool for predicting RNA secondary structure with consideration of sequence and contextual information.
Functional Genomics
- DAVID - a comprehensive set of functional annotation tools
- Enrichment analysis at the Gene Ontology Consortium web site
- GSEA - Gene Set Enrichment Analysis
- Enrichr - interactive and collaborative gene list enrichment analysis tool
- g:Profiler - a public web server for characterizing and manipulating gene lists
- BioGPS - gene annotation portal, a complete resource for learning about gene and protein function
- WebGestalt - WEB-based GEne SeT AnaLysis Toolkit
- PANTHER - Protein ANalysis THrough Evolutionary Relationships
- GeneMANIA - biological network integration for gene prioritization and predicting gene function
- InterMine - open source data warehouse system for the integration and analysis of biological data. Instances of InterMine automatically provide enrichment analysis for uploaded sets of genes
- IMPaLA - Integrated Molecular Pathway Level Analysis
- iLINCS - integrative genomics data portal
- CREEDS - CRowd Extracted Expression of Differential Signatures
Promoter Analysis
- GPminer - Gene Promoter Miner
- SoftBerry - Search for promoters/functional motifs
- TRANSFAC database-based search tools
Protein Analysis
- ProtParam - protein physical and chemical parameters
- SAPS - statistical analysis of protein sequences
- GPMAV lite - protein physical and chemical parameters
- ScanProsite - scans protein sequences for known functional motifs
- HAMAP - a system for the classification and annotation of protein sequences
- InterPro - functional analysis of proteins by classifying them into families and predicting domains and important sites
- ELM - annotation and detection of eukaryotic linear motifs
- MOTIF Search - protein motif search service
- NetPhos 3.1 - predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins
- KinasePhos2.0 - phosphorylation site prediction tool
- ProteinGuru - Global e-Utility and Resource Unit for Protein Research
Multiple Tools Websites
- ExPASy - bioinformatics resource portal
- Sequence Manipulation Suite - A collection of bioinformatics tools for manipulating and analyzing DNA sequences.
- DNA Tools - An online resource providing various tools for working with DNA sequences and data.
- FaBox - A tool for analyzing and visualizing DNA sequence features and annotations.
FREE SOFTWARE
In Silico Molecular Cloning
- Plasmid Editor (Exemplar ELN) - A tool for editing plasmids, integrated with Exemplar ELN.
- EMBOSS - The European Molecular Biology Open Software Suite.
- UGENE - A free bioinformatics software for molecular biology tasks.
- GenBeans - Software for molecular biology data analysis and visualization.
- Serial Cloner - A molecular biology software for cloning simulation.
- Gene Runner - A tool for DNA sequence analysis and manipulation.
- DNAStrider - DNA sequence analysis software with a focus on primer design.
- BioEdit - A biological sequence alignment editor.
- GENtle - A software suite for molecular biology tasks.
- pDRAW32 - A plasmid drawing software for molecular biologists.
- Visual Gene Developer - Software for gene design, visualization, and analysis.
- Jalview - A program for multiple sequence alignment and visualization.
- GeneStudio - Software for molecular biology and sequence analysis.
- ApE - A plasmid editor designed for Windows, macOS, and Linux.
Genomics, Transcriptomics, NGS Data
For comprehensive listings use dedicated websites, e. g. here.
Graphical user interface
- IGV - Integrative Genomics Viewer (NGS data visualization on genomes and more)
- Artemis - a free genome browser and annotation tool
- AltAnalyze - end-to-end analysis of single-cell and bulk RNA-Seq data
- FunRich - software tool used mainly for functional enrichment and interaction network analysis of genes and proteins
Command line interface
- Samtools - a suite of programs for handling high-throughput sequencing data files
- Cutadapt - removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from high-throughput sequencing reads
- STAR - ultrafast universal RNA-seq aligner
- HISAT2 - a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome)
- BBTools - a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data
- GeneSCF - Gene Set Clustering based on Functional annotation
- ANNOVAR - software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes
- GFFutils - a Python package for working with and manipulating the GFF and GTF format files
Cloud-based, with web browser interface
- Galaxy - web-based platform for data intensive biomedical research
- GenomeSpace - interoperability framework to support integrative genomics analysis through an easy-to-use Web interface
- GenePattern - provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis
- WebMeV - a cloud-based application supporting analysis, visualization, and stratification of large genomic data, particularly for RNA-Seq and microarray data
- BaseSpace - cloud-based genomics analysis and storage platform that directly integrates with all Illumina sequencers
Biological Systems Modeling
- Cytoscape - software platform for visualizing complex networks
- NetWalker - network analysis suite for functional genomics
- PathVisio - a tool to edit and analyze biological pathways
- CellDesigner - a modeling tool of biochemical networks
- COPASI - simulation and analysis of biochemical networks and their dynamics
- The Virtual Cell - virtual cell modeling & analysis
Statistical Data Analysis
- R - a free software environment for statistical computing and graphics
- PSPP - a program for statistical analysis of sampled data
- JASP - a free alternative to SPSS
- Past - free software for scientific data analysis
- Orange - open source data visualization and data analysis
- WinBUGS - flexible software for the Bayesian analysis of complex statistical models
- JAGS - a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation
- SHOGUN - a large scale machine learning toolbox
- ADaMSoft - a free system for data management, data and web mining, statistical analysis and more
Image Analysis and Graphics
General-purpose
- Fiji - open source image analysis software package
- GIMP - GNU Image Manipulation Program
- Inkscape - open-source professional vector graphics editor for Windows, Mac OS X and Linux
- SVG-Edit - fast, web-based, JavaScript-driven SVG drawing editor that works in any modern browser
- diagrams.net - an online diagram drawing tool
Cell microscopy-specific
- Cell Profiler - open-source software for quantitative analysis of biological images
- ilastik - interactive learning and segmentation toolkit
- CellTracker - an image processing software to perform automated, semi-automated, and manual cell migration detection
- AnaSP - a MATLAB software suite to analyse spheroids parameters
- LAS X LS - Leica LAS X Life Science
- ZEN Lite - free viewer for CZI files and other standard file types (Zeiss)
- NIS-Elements Viewer - free standalone program to view image files and datasets (Nikon)
PLASMID RESOURCES
Repositories and Vendors
- Addgene - a non-profit plasmid repository
- PlasmID Database - inexpensive sequence verified plasmid constructs
- Life Technologies vector selector
- VectorBuilder - custom vector cloning service
Maps and Sequences
- Addgene vector database
- DNA Sequences and Maps Tool at New England BioLabs
- SnapGene database of vector sequences
PROTOCOLS AND FORUMS
- EMBL protocols website - basic PCR and cloning protocols
- OpenWetWare - Wikipedia styled online protocols
- ResearchGate - a social network for scientists with a technical forum
- Biology-online forum - An online forum for discussions related to biology and life sciences.
- BioForum - A forum focused on discussions in molecular biology and related fields.
- BioTechniques forum - A platform for discussions on techniques and methods in molecular biology.