Molecular Tools

Most important sites

  • BD In-Fusion cloning (Selects 15bp overhangs for BD cloning primers)
  • BioCyc Database Collection
  • BLAST via NCBI
  • BRENDA The Comprehensive Enzyme Information System
  • EnsemblBacteria Over 30,000 genome sequences from bacteria and archaea have been annotated and deposited
  • Fitness browser check out the fitness of your gene of interest in numerous other organisms – large INSeq database covering many different organisms
  • Fluorescent proteins and their properties (fpbase)
  • Gecoviz: A tool you may find interesting to see whether the genomic context of your genes is conserved across bacteria.
  • In silico simulation of molecular biology experiments
  • KBase predictive biology open platform for comparative functional genomics and systems biology
  • KEGG (Kyoto Encyclopedia of Genes and Genomes. Find ezymes and cross-links from all the genome projects)
  • MicrobesOnline (great tool for genome comparison and gene analysis)
  • MG-RAST metagenomics analysis server
  • NCBI (Pubmed, Entrez etc)
  • Plant Metabolic Network
  • RhizoDB
  • Rlv3841 annotation (Latest annotation as an Excel spreadsheet)
  • SalisLab RBS Calculator
  • STRING – Known and Predicted Protein-Protein Interactions
  • TransportDB – Genomic Comparisons of Membrane Transport Systems (Paulson’s site)
  • Wellcome Trust Sanger Institute

Alphabetical listing of all sites

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