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 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
  • RefGene - a gene database with comprehensive gene-related information
  • 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

GENE MUTATIONS AND VARIATIONS

  • dbSNP - a database of single nucleotide polymorphisms (SNPs) and small-scale insertions/deletions, microsatellites, and non-polymorphic variants.
  • MutDB - a database for assessing the impact of genetic variants
  • HGMD - The Human Gene Mutation Database
  • COSMIC - the Catalogue Of Somatic Mutations In Cancer
  • GWAS Central - a centralized compilation of summary level findings from genetic association studies
  • DGV - a curated catalogue of human genomic structural variation

EPIGENETICS

GENE REGULATORY ELEMENTS

  • TRED - Transcriptional Regulatory Element Database
  • 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

NON-CODING RNA DATABASES AND TOOLS

  • miRBase - a searchable database of published miRNA sequences and annotation
  • starBase - decoding interaction networks of lncRNAs, miRNAs, competing endogenous RNAs, RNA-binding proteins and mRNAs
  • 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

PROTEIN FUNCTION AND REGULATION

  • KEGG PATHWAY Database
  • NetPath - manually curated resource of signal transduction pathways in humans
  • Reactome - a signaling pathway database
  • Phospho.ELM - phosphorylation site database
  • PHOSIDA - phosphorylation site database
  • dbPAF - database of phospho-sites in animals and fungi
  • PhosphoNET - human phosphosite knowledgebase
  • IntAct - a protein interaction database at EBI
  • BioGRID - a repository for interaction datasets
  • STRING - known and predicted protein-protein interactions

STRUCTURE DATABASES

OTHER RESOURCES


ONLINE TOOLS

SEQUENCE ALIGNMENT

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
  • WebGestalt - WEB-based GEne SeT AnaLysis Toolkit
  • PANTHER - Protein ANalysis THrough Evolutionary Relationships
  • Galaxy - web-based platform for data intensive biomedical research
  • GeneMANIA - biological network integration for gene prioritization and predicting gene function

PROMOTER ANALYSIS

PROTEIN ANALYSIS

  • ProtParam - protein physical and chemical parameters
  • SAPS - statistical analysis of protein sequences
  • 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
  • GPMAV lite - protein physical and chemical parameters

MULTIPLE TOOLS WEBSITES


FREE SOFTWARE

IN SILICO MOLECULAR CLONING

GENOMICS SOFTWARE

  • IGV - Integrative Genomics Viewer (NGS data visualization on genomes and more)
  • Artemis - a free genome browser and annotation tool

BIOLOGICAL SYSTEMS MODELING

  • Cytoscape - software platform for visualizing complex networks
  • NetWalker - network analysis suite for functional genomics
  • 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 asystem for data management, data and web mining, statistical analysis and more

IMAGE ANALYSIS

  • Fiji - open source image analysis software package
  • Cell Profiler - open-source software for quantitative analysis of biological images
  • CellTracker - an image processing software to perform automated, semi-automated, and manual cell migration detection

PLASMID RESOURCES

REPOSITORIES AND VENDORS

MAPS AND SEQUENCES


ONLINE PROTOCOLS AND FORUMS


info@molbiotools.com

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