molbiotools
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Molbiotools is a collection of free online apps:

DNA Sequence Tools
Text and Data Tools
Lab Calculators
Math Calculators

DATABASES

Nucleotide and Protein Sequences

  • Genbank - Nucleotide sequence database at NCBI
  • ENA - European Nucleotide Archive at EMBL-EBI
  • DDBJ - DNA Data Bank of Japan
  • Protein database at NCBI
  • UniProt - a resource of protein sequence and functional information

Genome Downloads

Genome Browsers

Gene Databases

  • Gene - a gene database at NCBI
  • UniGene - a transcript database at NCBI
  • SOURCE - a gene database
  • GeneAtlas - a gene database
  • GeneCards - human gene database
  • OMIM - An Online Catalog of Human Genes and Genetic Disorders
  • AmiGo - a gene ontology database
  • HGNC - HUGO Gene Nomenclature Committee
  • GENCODE - human and mouse gene annotation database
  • Harmonizome - integrated knowledge about genes and proteins

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

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

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


ONLINE TOOLS

Sequence Alignment

PCR primer design

siRNA/shRNA Design

CRISPR Design

RNA Secondary Structure Prediction

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

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


FREE SOFTWARE

In Silico Molecular Cloning

Genomics, Transcriptomics, NGS Data

Just a few examples. 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

Maps and Sequences


ONLINE PROTOCOLS AND FORUMS


bioinformatics tools for protein analysis