Bioinformatics Resource Tools
A categorized collection of essential bioinformatics tools and databases
Sequence Alignment & BLAST
| Tool | Description | Notes |
|---|
| NCBI BLAST |
The standard tool for sequence similarity search of nucleotide/protein sequences |
Web / Local |
| EMBOSS Needle/Water |
Global and local pairwise sequence alignment |
Web |
| Minimap2 |
Ultra-fast alignment tool for long-read sequences |
Command-line |
| Bowtie2 |
Short-read aligner, commonly used in RNA-seq/ChIP-seq preprocessing |
Command-line |
| BWA / BWA-MEM |
Standard tool for aligning NGS reads to a reference genome |
Command-line |
Multiple Sequence Alignment & Phylogenetics
| Tool | Description | Notes |
|---|
| Clustal Omega |
Leading tool for multiple sequence alignment (MSA) |
Web / Local |
| MAFFT |
High-speed MSA program well suited for large datasets |
Web / Local |
| iTOL |
Visualization and annotation of phylogenetic trees |
Web |
| IQ-TREE |
Maximum-likelihood based phylogenetic tree inference |
Command-line |
| MEGA |
All-in-one GUI software for phylogenetic analysis, beginner-friendly |
Desktop |
| Jalview |
GUI tool for editing/visualizing multiple sequence alignments and building trees |
Desktop |
| CIBIV Software |
Collection of phylogenetics/sequence analysis software (University of Vienna) |
Software collection |
Genome Browsers
| Tool | Description | Notes |
|---|
| UCSC Genome Browser |
Leading browser for visualizing genome data across many species |
Web |
| Ensembl |
Provides gene annotation and comparative genomics data |
Web |
| IGV (Integrative Genomics Viewer) |
Directly visualize alignment results such as BAM/VCF files |
Desktop / Web |
| JBrowse 2 |
Web-based, highly customizable genome browser |
Web |
NGS & Variant Calling
| Tool | Description | Notes |
|---|
| GATK |
Standard toolkit/pipeline for variant calling (SNP/Indel) |
Command-line |
| SAMtools / BCFtools |
Essential utilities for processing SAM/BAM/VCF files |
Command-line |
| SnpEff / SnpSift |
Variant annotation and functional impact prediction |
Command-line |
| fastp |
Quality control and trimming (preprocessing) of NGS reads |
Command-line |
| FastQC |
Generates quality-check reports for sequencing data |
Command-line / GUI |
RNA-seq & Expression Analysis
| Tool | Description | Notes |
|---|
| Salmon |
Ultra-fast transcript-level quantification |
Command-line |
| HISAT2 |
Splice-aware alignment tool for RNA-seq reads |
Command-line |
| DESeq2 |
R package for differential expression analysis |
R / Bioconductor |
| edgeR |
R package for count-based differential expression analysis |
R / Bioconductor |
| GSEA |
Gene Set Enrichment Analysis software |
Desktop |
Protein Structure & Structural Biology
| Tool | Description | Notes |
|---|
| RCSB PDB |
Protein Data Bank — repository of experimental protein structures |
Database |
| AlphaFold DB |
Database of AI-predicted protein structures |
Web / DB |
| PyMOL |
3D molecular structure visualization software |
Desktop |
| ChimeraX |
Advanced molecular visualization and analysis tool |
Desktop |
| SWISS-MODEL |
Automated server for protein homology modeling |
Web |
| SWISS-MODEL Interactive |
Interactive modeling mode with manual template selection |
Web |
| AlphaFold2 (ColabFold) |
Free notebook for running structure prediction on Google Colab |
Colab |
| CATH |
Protein domain structure classification database |
Database |
| AutoDock Vina |
Molecular docking software for protein-ligand simulations |
Software |
Membrane Protein Structure & Prediction
| Tool | Description | Notes |
|---|
| DTU Health Tech |
Portal of prediction services including SignalP, TMHMM, and more |
Web portal |
| DeepTMHMM |
Deep-learning based transmembrane helix prediction |
Web |
| MPEx |
Membrane protein topology exploration based on hydrophobicity analysis |
Web |
| MemBrain |
Server for membrane protein topology and helix prediction |
Web |
| mpstruc |
Database of membrane proteins with solved structures |
Database |
| OPM |
Database of protein orientations within the lipid membrane |
Database |
| PDBTM |
Database dedicated to transmembrane proteins within the PDB |
Database |
| MemProtMD |
Database of molecular dynamics (MD) simulations for membrane proteins |
Database |
Protein Domain & Motif Databases
| Tool | Description | Notes |
|---|
| InterPro |
Integrated search across protein families, domains, and functional sites |
Web |
| Prosite |
Database of protein sequence motifs and profiles |
Database |
| Protein CDD |
NCBI’s Conserved Domain Database |
Database |
| SMART |
Analysis tool for signaling and extracellular protein domains |
Web |
| HAMAP |
Automated annotation system for microbial protein families |
Database |
| NCBIfam |
NCBI’s database of protein family models |
Database |
Virus Structure & Information Databases
| Tool | Description | Notes |
|---|
| VIPERdb |
Database dedicated to virus capsid structures |
Database |
| ViralZone |
Encyclopedia of viral taxonomy, genomes, and proteins |
Database |
Expression Atlas
| Tool | Description | Notes |
|---|
| Human Protein Atlas |
Map of human protein expression by tissue and cell type |
Web |
| Allen Brain Atlas |
Database of gene expression maps in brain tissue |
Web |
| GTEx Portal |
Database of tissue-specific gene expression and eQTL data |
Web |
Functional Annotation & Enrichment Analysis
| Tool | Description | Notes |
|---|
| DAVID |
Platform for functional annotation and enrichment analysis of gene lists |
Web |
| QuickGO |
Browser for searching Gene Ontology (GO) terms and annotations |
Web |
| Venn (VIB/UGent) |
Tool for comparing gene lists using Venn diagrams |
Web |
| Venny |
Venn diagram tool supporting up to four lists |
Web |
Variant-Disease Association & Target Discovery
| Tool | Description | Notes |
|---|
| SNP&GO |
Predicts the disease association of single amino acid variants |
Web |
| Open Targets |
Platform integrating gene-disease evidence for drug target discovery |
Web |
| dbGaP |
Repository of genotype-phenotype association study data |
Database |
Data Repositories & Integrated Portals
| Tool | Description | Notes |
|---|
| NCBI |
Integrated portal for biological data including GenBank and PubMed |
Database |
| UniProt |
Database of protein sequence and functional information |
Database |
| GEO (Gene Expression Omnibus) |
Public repository of expression data (microarray/RNA-seq) |
Database |
| ENA (European Nucleotide Archive) |
European archive of nucleotide sequence data |
Database |
| GDC (Genomic Data Commons) |
Data portal for cancer genomics projects such as TCGA |
Database |
| EBI Data Resources & Tools |
Complete listing of all databases/tools provided by EBI |
Web portal |
| OmicsDI |
Search across multi-omics datasets (genomics/proteomics/metabolomics) |
Web |
| BioSamples |
Integrated repository of biological sample metadata |
Database |
| NIH RePORTER |
Search NIH-funded research projects, useful for tracking research trends |
Web |
Pathway & Network Analysis
| Tool | Description | Notes |
|---|
| KEGG |
Database of metabolic pathways and gene networks |
Database |
| STRING |
Analysis of protein-protein interaction networks |
Web |
| Cytoscape |
Software for visualizing and analyzing biological networks |
Desktop |
| Reactome |
Curated database of biological pathways |
Database |
Primer Design & Cloning Tools
| Tool | Description | Notes |
|---|
| Primer-BLAST |
PCR primer design and specificity checking (NCBI) |
Web |
| Primer3 |
Most widely used open-source primer design engine |
Web / Local |
| SnapGene |
Plasmid mapping and cloning simulation software |
Desktop (paid / free viewer) |
| Benchling |
Integrated platform for lab notebooks and molecular cloning |
Web |
Educational & Reference Resources
| Tool | Description | Notes |
|---|
| Webvision |
Online textbook on the structure and function of the retina and visual system |
Educational resource |
Life and Biology stories with Sooyoung and Others 