| title | description | published | date | tags | editor | dateCreated |
|---|---|---|---|---|---|---|
VDC Favorites |
A selection of the favorite websites of the VDC Lab |
true |
2023-12-27 18:15:37 UTC |
reference, resource reference |
markdown |
2020-04-15 18:50:25 UTC |
Here you can find a curated selection of the tools and websites presented by this wiki. This collection is dedicated to the preferred resources of Dr. Valérie de Crécy-Lagard. {.is-info}
- GUIDANCE2 Weighting, filtering or masking unreliably aligned positions in sequence alignments before subsequent analysis {.links-list}
- EMBL-EBI Multiple Sequence Alignment
- MAFFT Multiple alignment program for amino acid or nucleotide sequences
- MultAlin MSA from a group of related sequences using progressive pairwise alignments
- PSSMSearch Web application to discover novel protein motifs (SLiMs, mORFs, miniMotifs) and PTM sites
- T-COFFEE Align Protein, DNA and RNA sequences {.links-list}
- Dotlet JS Comparing sequences by the diagonal plot method
- Pairwise Alignment Basic protein pairwise alignment tool
- PRSS Evaluates the significance of a protein sequence alignment {.links-list}
- GeneMark Web page hosting families of gene prediction programs
- IslandViewer Integrates four different genomic island prediction methods: IslandPick, IslandPath-DIMOB, SIGI-HMM, and Islander
- ORFfinder Searches for open reading frames (ORFs) in the DNA sequence you enter {.links-list}
- KEGG-Annotation Database contains three main components for genome/metagenome annotation
- proGenomes2 Consistently annotated bacterial and archaeal genomes {.links-list}
- MetaCyc Curated database of experimentally elucidated metabolic pathways
- Pathguide Provides an overview of more than 190 biological pathway and network databases
- SimpleClinVar Web server to explore and retrieve gene and disease variants aggregated in ClinVar database {.links-list}
- BioCyc Collection of 16,822 Pathway/Genome Databases (PGDBs)
- BRENDA ENZYMES Main collection of enzyme functional data available
- CATH Classification of protein structures downloaded from the Protein Data Bank
- DEG Database of Essential Genes
- FungiDB Fungus database
- JGI GOLD Genomes Online Database
- QuartataWeb User-friendly server developed for polypharmacological and chemogenomics analyses
- SCOPe Database developed at the Berkeley Lab and UC Berkeley
- SEED Viewer Allows users to access the latest curated datasets for comparative genomics {.links-list}
- Database_Commons Provides users with access to a collection of publicly available biological databases
- DoriC A database of oriC regions in bacterial genomes
- ECOD Hierarchical classification of protein domains according to their evolutionary relationships
- InterPro Functional analysis of proteins by classifying them into families and predicting domains
- JGI Joint Genome Institute - Main webiste
- KBase Large-scale bioinformatics system that enables users to upload their own data
- NCBI National Center for Biotechnology Information - Main website
- NPAtlas Designed to cover all microbially-derived natural products published
- RPFdb Public resource for hosting, analyzing and visualizing ribosome profiling (Ribo-seq) data
- UniProt Comprehensive resource for protein sequence and annotation data {.links-list}
- Arabidopsis Information Resource (TAIR) database of genetic and molecular biology data for A. thaliana
- CellMap Storing and visualizing genetic interactions in S. cerevisiae
- HumanMine An integrated database of Homo sapiens genomic data
- neXtProt Exploring the universe of human proteins
- PomBase Scientific resource for fission yeast
- Saccharomyces Genome Database Comprehensive integrated biological information for the budding yeast S. cerevisiae
- SEEK Computational gene co-expression search engine
- SPELL Query-driven search engine for large gene expression microarray compendia on S. cerevisiae {.links-list}
- BacMap An Interactive Atlas for Exploring Bacterial Genomes
- eLMSG Intended to integrate microbial systematics, genomics and phenomics
- PATRIC Data and analysis tools to support biomedical research on bacterial infectious diseases
- PubSEED SEED is a constantly updated integration of genomic data {.links-list}
- AureoWiki Repository of the Staphylococcus aureus research & annotation
- EcoCyc Scientific database for the bacterium Escherichia coli K-12 MG1655
- Pseudomonas Genome DB Genome annotation and genome analysis data of Pseudomonas
- SubtiWiki Relational database of B. subtilis
- SynWiki Dedicated to the current generated functional annotation of the synthetic organism JCVI-syn3.0/syn3A
- TB Genomes Database An integrated platform for Tuberculosis research {.links-list}
- JGI-IMG/Virus Community resource for analysis and annotation of genome
- PHASTER Rapid identification and annotation of prophage sequences within bacterial genomes and plasmids {.links-list}
- ATTED-II Coexpression database for plants to discover relationships of unknown genes within a species
- COXPRESdb Database providing coexpression information for 11 animal species {.links-list}
- KofamKOALA Assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam
- OrthoMCL OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences {.links-list}
- Chemgen Searching of growth data (strains/condition) of various E. coli
- CTD Advance understanding about how environmental exposures affect human health
- FitDB Searchable database of quantitative chemical-genetic interactions
- FitnessBrowser Browse thousands of genome-wide fitness experiments from diverse bacteria
- GeneCards The Human Gene Database
- OGEE Aims to enhance our understanding of the essentiality of genes
- VarSite Aims to annotate known disease-associated variants in human genes with structural information {.links-list}
- APID Agile Protein Interactomes DataServer gives a thorough collection of protein interactomes
- ComplexPortal Curated encyclopaedic resource of macromolecular complexes from a number of key model organisms {.links-list}
- RegPrecise database for capturing, visualization and analysis of transcription factor regulons
- RegulonDB Database on transcriptional regulation in Escherichia coli K-12 containing knowledge {.links-list}
- 3dmodmap Database of maps showing the sites of modified rRNA nucleotides in 3D models
- GtRNAdb tRNA database contains tRNA gene predictions made by the program tRNAscan-SE
- Modomics Database of RNA modifications
- The RNA Modification Database Listing of posttranscriptionally modified nucleosides from RNA
- T-Psi-C Allows you to search across all available tRNA sequences
- UCSC GtRNAdb tRNAscan-SE analysis of complete genomes {.links-list}
- ORENZA Accurate and up to date list of Enzyme Activities for which no sequences are available
- Orphan Enzyme Project Associate an amino-acid sequence with every known orphan enzyme {.links-list}
- Connected Papers Explore connected papers in a visual graph
- PaperBLAST database of protein sequences that are linked to scientific articles
- PubMed Advanced Search Builder Builder to do advanced search on PubMed {.links-list}
- Graph Splitting Phylogenetic analysis method, which can effectively resolve early evolution of protein families
- IQ-TREE Efficient software for phylogenomic inference
- NGPhylogeny Reconstructing and analysing phylogenetic relationships
- Simple Phylogeny Provides access to phylogenetic tree generation methods from the ClustalW2
- TREND Resource that can calculate gene neighborhoods {.links-list}
- AnnoTree Visualization of genome annotations across large phylogenetic trees
- OrthoInspector Inference of orthologous relationships between protein coding-genes {.links-list}
- Lifemap Tool allowing the exploration of a complete representation of the Tree of Life {.links-list}
- Open Targets Comprehensive and robust data integration resource for access and visualization of drug targets {.links-list}
- PLAZA Online platform for plant comparative genomics {.links-list}
- ArDock Detect interaction sites by docking arbitrary proteins
- Skolnick Tools Suite Suite of tools designed, produced, and made available by the Skolnick Lab
- Zhou Group Tools Suite of tools for prediction of protein-protein interactions {.links-list}
- RadicalSAM Exploring the Radical SAM Enzyme Superfamily {.links-list}
- BioNumbers Quick-reference of common values and metrics frequently used in research via methods, study systems, and/or techniques
- EMBL-EBI Services, databases, and tools; facilitates fundamental and translational research and provides professional training and learning materials for bioinformatics
- EZBioCloud ChunLab's public data and analytics portal
- FAIRsharing A curated, informative and educational resource on data and metadata standards
- NCBI All Resources
- NCBI Search engine
- NAR Database Summary Category list
- Online Bioinformatics Resources Collection Contains annotations and links for 2449 bioinformatics databases and software tools
- RTH Analysis of the mammalian genome for non-coding RNAs in relation to (inflammatory) diseases {.links-list}
- BahlerLab Tools for analyzing S. pombe genetics and genetic regulation
- BLAT Search Genome Quickly find sequences of 95% and greater similarity of length 25 bases or more {.links-list}
- Phylogenes Pre-computed phylogenetic trees of gene families alongside experimental gene function data {.links-list}
- ABCDdb ABCD database is a manually curated depository of sequenced antibodies
- ApE Tool that allows information and editing of plasmids, as well as tools for data visualization
- NEBcutter Take DNA sequence and find the large, open reading frames using the E.coli genetic code
- Primer3Plus Pick primers from a DNA sequence
- Primer-BLAST A tool for finding specific primers {.links-list}
- Genoscope Microscope Phyloprofile Allows to search for common OR specific genes between genomes
- JGI-IMG-Phylogeny Assess phylogenetic composition of a metagenome sample based {.links-list}
- ExPASy Proteomics Bioinformatic resources for proteomics
- SFLD Hierarchical classification of enzymes that relates specific sequence-structure features {.links-list}
- Nucleic Acid Sequence Massager Tool to manipulate sequence(s) in fasta format
- Sequence Manipulation Suite Sequence Manipulation Suite of bioinformatics.org {.links-list}
- BindUP Predicting DNA and RNA binding proteins using the electrostatic patches on the protein surface {.links-list}
- GalaxyWEB Web server for protein structure prediction, refinement, and related methods
- IntFOLD Web resource for high performance protein structure and function prediction
- RaptorX Protein structure prediction server {.links-list}
- RNAcentral The non-coding RNA sequence database {.links-list}
- Aquaria Allows for the visualization of protein structure of various proteins from numerous species
- iCn3D Viewer for interactive viewing of three-dimensional macromolecular structures and chemicals
- Phyre Web-based services for protein structure prediction
- RCSB-PDB Makes PDB data available at no charge to all data consumers
- SWISS-MODEL Web-based integrated service dedicated to protein structure homology modelling {.links-list}
- CARD Database of antibiotic resistance genes, their products and associated phenotypes
- CD-Search Searching the Conserved Domain Database with protein or nucleotide query sequences
- Compute pI Allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight)
- 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
- Genoscope - MicroScope MicroScope offers many useful data-exploring functionalities
- MolBiol-Tools Online tools and resources for molecular biologists
- MEME-Suite Discover novel motifs in collections of unaligned nucleotide or protein sequences
- MitoMiner Database of mammalian mitochondrial localisation evidence, phenotypes, and diseases
- NCBI Conserved-Domains
- NPS@ An interactive web server dedicated to protein sequence analysis.
- Phobius Prediction of transmembrane topology and signal peptides
- PROSITE Database of protein families and domains
- ProteomeHD Protein Co-regulation Analysis
- PSORTb Precise bacterial localization prediction tool
- 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
- TMHMM Prediction of transmembrane helices in proteins
- TopSearch Gateway to protein structures and their structural relationships
- Zhang Lab Web page dedicated to the research, publications, information of the Zhang Lab {.links-list}
- SIAS Calculates pairwise sequence identity and similarity from multiple sequence alignments {.links-list}
- Benchling Electronic notebook and a suite of sequence design tools for free to academics {.links-list}
- 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 {.links-list}
- bioDBnet-db2db Database to Database Conversions
- UniProt-Mapping Very usuful tool when you want to swap IDs from a database to another {.links-list}
- Sequence Massager Easy modification and editing of user-inputted nucleic acid sequences {.links-list}
- 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 {.links-list}
- 3did 3D interacting domains (3did) is a catalog of protein–protein interactions
- EcoliNet Probabilistic functional gene network for Escherichia coli
- GeneMANIA Predict the functions of your favorite genes and gene sets
- IMP Analyze your experimental results in the functional context of gene-gene networks {.links-list}
- GO Enrichment Analysis Representation of our current scientific knowledge about the functions of genes {.links-list}
- AACompIdent Allows the identification of a protein from its amino acid composition
- ArDock etect interaction sites by docking arbitrary proteins
- COGcollator Web server for analysis of distant relationships between homologous protein families
- GapMind Automated annotation of Amino acid biosynthesis
- Genome3D Provides consensus structural annotations and 3D models for sequences
- RNAmmer Predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences
- tRNAscan-SE Searching for tRNA genes in genomic sequence
- TXSSdb Database of detected potential secretion systems in bacterial genomes {.links-list}
- PaintOmics Integrative visualization of multiple omic datasets onto KEGG pathways
- PathView Provides easy interactive access, and generates high quality, hyperlinked graphs {.links-list}
- Bioinformatics Club Bioinformatics Course Regular expression for Biology
- Biostars Forum based on the Stack Exchange on problems of bioinformatic {.links-list}
- NCBI Tutorial page {.links-list}
- Clustergrammar Analyzing high-dimensional data as interactive hierarchically clustered heatmaps
- Heatmapper Online application for visualizing various types of data as heat maps
- Jalview Program for multiple sequence alignment editing {.links-list}
- GCTNG Visualize the genomic context of a gene or a group of genes and their orthologous relationships
- Gene Graphics Application that allows for visually representations of physical gene neighborhoods {.links-list}
- IBS Assisting experimentalists in drawing publication-quality diagrams of both protein and nucleotide sequences {.links-list}
- Seq2Logo Sequence logo generator {.links-list}
- MView Reformats the results of a sequence database search or a multiple alignment
- Two Sample Logos Calculates and visualizes differences between two sets of aligned samples of amino acids or nucleotides {.links-list}
- Cn3D Allows you to view 3-dimensional structures from NCBI's Entrez Structure database
- JPred A Protein Secondary Structure Prediction Server {.links-list}
- EvolView Easy-to-use online tool for displaying, managing and customizing phylogenetic trees
- iTOL Online tool for the display, annotation and management of phylogenetic trees
- Phylo.io Visualising and comparing phylogenetic trees {.links-list}
- BEG-Venn An interactive tool for comparing lists with Venn's diagrams
- BioVenn Comparison and visualization of biological lists using area-proportional Venn diagrams
- OrthoVenn2 Platform for comparison and annotation of orthologous gene clusters among multiple species
- Stefanjol Venny Online venn diagram generator
- Venny An interactive tool for comparing lists with Venn's diagrams {.links-list}