¶ Tools
¶ Alignment tools
Dotlet JS Comparing sequences by the diagonal plot method- Clustal Omega MSA program that uses seeded guide trees and HMM profile-profile techniques
- EMBL-EBI Multiple Sequence Alignment
- GUIDANCE2 Weighting, filtering or masking unreliably aligned positions in sequence alignments before subsequent analysis
- LALIGN Find multiple matching subsegments in two sequences
- LAST LAST finds similar regions between sequences
- MAFFT Multiple alignment program for amino acid or nucleotide sequences
- MultAlin MSA from a group of related sequences using progressive pairwise alignments
- MView Reformats the results of a sequence database search or a multiple alignment
- Pairwise Align DNA Basic DNA pairwise alignment tool
- Pairwise Align Protein Basic protein pairwise alignment tool
- Pairwise Alignment Basic protein pairwise alignment tool
- PRSS Evaluates the significance of a protein sequence alignment
- RibEx Search any sequence for known riboswitches as well as other predicted bacterial regulatory elements
- SIAS Calculates pairwise sequence identity and similarity from multiple sequence alignments
- T-COFFEE Align Protein, DNA and RNA sequences
¶ Analysis Tools
- CARD Database of antibiotic resistance genes, their products and associated phenotypes
- CD-Search Searching the Conserved Domain Database with protein or nucleotide query sequences
- Center for the Study of Systems Biology Dedicated to the research interests, publications around Jeffrey Skolnick
- CMBL MotLoc Uses aligned set of DNA sequence motifs and finds similar motifs in the analyzed sequence
- Compute pI Allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight)
- EmExplorer Exploring time activation of gene expression in mammalian embryos
- ENDscript Extracts and renders a comprehensive analysis of primary to quaternary protein structure information
- Enzyme Function Initiative (EFI) Creating and interacting with sequence similarity networks
- ESPript Program which renders sequence similarities and secondary structure information from aligned sequences
- ETviewer Relative rank of functional and structural importance among protein homologs sequence positions
- FungiPath Orthologous proteins in fungal genomes database
- Genoscope - MicroScope MicroScope offers many useful data-exploring functionalities
- IDDomainSpotter Sequence-based approach to assess and visualize domain organisation
- MolBiol-Tools Online tools and resources for molecular biologists
- MEME-Suite Discover novel motifs in collections of unaligned nucleotide or protein sequences
- MetNetDB Information on networks of metabolic and regulatory and interactions in Arabidopsis
- MitoMiner Database of mammalian mitochondrial localisation evidence, phenotypes, and diseases
- NCBI Conserved Domains
- NetGO Improves large-scale AFP with massive network information
- nf-core A community effort to collect a curated set of analysis pipelines built using Nextflow
- NPS@ An interactive web server dedicated to protein sequence analysis.
- PDBeMotif Fast and powerful search tool that facilitates exploration of the Protein Data Bank (PDB)
- Phobius Prediction of transmembrane topology and signal peptides
- PROSITE Database of protein families and domains
- ProteomeHD Protein Co-regulation Analysis
- ProtFus Resource that has information about fusion proteins and their interactions
- PSORTb Precise bacterial localization prediction tool
- RDP Aligned and annotated Bacterial and Archaeal 16S rRNA sequences
- SignalP Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
- SoftBerry Tools for genomic using computational methods of high throughput biomedical data analysis
- String Protein-Protein Interaction Networks and Functional Enrichment Analysis
- SynMap Generates a syntenic dotplot between two organisms and identifies syntenic regions
- TargetP Subcellular location of proteins: mitochondrial, chloroplastic, secretory pathway
- TISSUES Tissue expression database
- TMHMM Prediction of transmembrane helices in proteins
- TopSearch Gateway to protein structures and their structural relationships
- ViennaRNA Several stand-alone programs for the prediction and comparison of RNA secondary structures
- Zhang Lab Web page dedicated to the research, publications, information of the Zhang Lab
¶ Cloning Tools Platforms
- Addgene Global, nonprofit repository that was created to help scientists share plasmids
- Benchling Electronic notebook and a suite of sequence design tools for free to academics
- Serial Cloner Intuitive interface that assists you in DNA cloning, sequence analysis and visualization
¶ Creating Or Finding Sequence Logos
- Berkeley WebLogo Designed to make the generation of sequence logos as easy and painless as possible
- Skylign Creating logos representing both sequence alignments and profile hidden Markov models
- WebLogo3 Take multiple sequence alignments and generate a graphical representation of the consensus
¶ Database Linker
- bioDBnet-db2db Database to Database Conversions
- BioGPS Extensible and customizable gene annotation portal
- LinkDB database of links
- UniProt-Mapping Very usuful tool when you want to swap IDs from a database to another
¶ Data formatting
- EMBOSS Seqret Extracting sequences from databases, displaying sequences, reformatting sequences
- Reverse Complement Converts a DNA sequence into its reverse, complement, or reverse-complement
- Sequence Massager Easy modification and editing of user-inputted nucleic acid sequences
- XSuLT Annotation and formatting of a multiple protein sequence alignment or single structure
¶ Gene finders
- BLAST Finds regions of local similarity between sequences
- Genevisible Find the top tissues, cell lines, cancers or perturbations for your gene of interest
- HMMER Fast and sensitive homology searches
- InterMine Integrates biological data sources, making it easy to query and analyse data
- ProtPhylo Web server to retrieve phenotype-to-protein and protein-to-protein functional associations
¶ Gene Neighborhoods
- FunGeco Functional potential of bacterial genomes and microbiomes from gene context information
- Phagonaute Phagonaute is a new phage genome browser
¶ Gene Networks
- 3did 3D interacting domains (3did) is a catalog of protein–protein interactions
- AraNet Functional gene network for Arabidopsis thaliana
- COMPLEAT Online tool used to analyze high-throughput datasets using protein complex enrichment analysis
- EcoliNet Probabilistic functional gene network for Escherichia coli
- GeneMANIA Predict the functions of your favorite genes and gene sets
- GPS-Prot Data Visualization for Protein-Protein Interactions
- IMP Analyze your experimental results in the functional context of gene-gene networks
¶ Gene Ontology Enrichment Tools
- AgriGO Web-based tool and database for gene ontology analyses
- DAVID Database for Annotation, Visualization and Integrated Discovery
- DeepGOPlus Predicting protein functions based on protein sequence
- DiVenn Venn diagram is widely used to compare gene lists between multiple experiments
- GO Enrichment Analysis Representation of our current scientific knowledge about the functions of genes
- GOrilla Identifying and visualizing enriched GO terms in ranked lists of genes
- Metascape A Gene Annotation & Analysis Resource
- PRO Ontological representation of protein-related entities by explicitly defining them and showing the relationships
- The BAR Explore large-scale data sets from Arabidopsis and other species, and for hypothesis generation
- YeastEnrichr New gene list enrichment analysis tool for Saccharomyces cerevisiae
¶ Motifs Analysis Tools
- Domain mapping of disease mutations Database in which each disease mutation can be displayed by its gene
- MyHits Hits is a free database devoted to protein domains
¶ Phylogeny Tools
- BCdatabaser Pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data
- Graph Splitting Phylogenetic analysis method, which can effectively resolve early evolution of protein families
- IQ-TREE Efficient software for phylogenomic inference
- LeBIBI-QBPP Quick Bioinformatic Phylogeny of Prokaryotes web-server
- MEGASoftware Software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees
- NGPhylogeny Reconstructing and analysing phylogenetic relationships
- Phylemon Web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
- Simple Phylogeny Provides access to phylogenetic tree generation methods from the ClustalW2
¶ Phylogenetic Distribution Tools
- AnnoTree Visualization of genome annotations across large phylogenetic trees
- JGI-IMG/Microbes Community resource for analysis and annotation of genome
- JGI-IMG/Virus Community resource for analysis and annotation of genome
- KEGG Ortholog Cluster Database of ortholog clusters (OCs) based on the whole genome comparison
- OrthoDB OrthoDB presents a catalog of orthologous protein-coding genes
- OrthoInspector inference of orthologous relationships between protein coding-genes
¶ Prediction
- AACompIdent Allows the identification of a protein from its amino acid composition
- AtSubP Arabidopsis Subcellular Localization Prediction Server
- COGcollator Web server for analysis of distant relationships between homologous protein families
- EffectiveDB Prediction of bacterial protein secretion
- GapMind Automated annotation of Amino acid biosynthesis
- Genome3D Provides consensus structural annotations and 3D models for sequences
- miRPD Explicitly inferring miRNA-protein-disease associations
- MMTK Open Source program library for molecular simulation applications
- ProtParam Allows the computation of various physical and chemical parameters for a given protein
- RNAmmer Predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences
- RNApredator Bacterial sRNA target prediction webserver
- TRED Collects cis - and trans -regulatory elements and is dedicated to easy data access and analysis
- tRNAscan-SE Searching for tRNA genes in genomic sequence
- TXSSdb Database of detected potential secretion systems in bacterial genomes
¶ Tools to Make Figures
- Caleydo Tools that focuses on biological data visualization
- Clustergrammar Analyzing high-dimensional data as interactive hierarchically clustered heatmaps
- ETE-Toolkit A Python framework for the analysis and visualization of trees
- EvolView Easy-to-use online tool for displaying, managing and customizing phylogenetic trees
- GraPhlAn Tool that produces high-quality, compact visualizations of microbial genomes
- Heatmapper Online application for visualizing various types of data as heat maps
- iTOL Online tool for the display, annotation and management of phylogenetic trees
- PCAGO Analyzing your RNA-Seq read counts with principal component analysis (PCA)
- Phylo.io Visualising and comparing phylogenetic trees
¶ Visualizing Pathways - No Data Mapping
¶ Visualizing Pathways - Mapping Data To Pathways
- ConsensusPathDB Integrates interaction networks in Homo sapiens
- GENIES Predict potential functional associations between genes
- KEGG-Mapper Collection of tools for KEGG mapping
- PaintOmics Integrative visualization of multiple omic datasets onto KEGG pathways
- PathView Provides easy interactive access, and generates high quality, hyperlinked graphs
- Pathway-Commons Access and discover data integrated from public pathway and interactions databases