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
- ExPASy (GO HERE FIRST FOR ANY MOL BIOL RESOURCE)
- 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
- ABCdb Archaeal and Bacterial ABC Systems database
- American Type Culture Collection (ATCC) The Global Bioresources Center
- Atlas of Biochemistry
- BD In-Fusion cloning (Selects 15bp overhangs for BD cloning primers)
- Biochemical Pathway Maps
- BioCyc Database Collection
- BLAST via NCBI
- BRENDA The Comprehensive Enzyme Information System
- ChemBioFinder
- DAS Transmembrane Prediction Server
- EBI (European Bioinformatics Institute, go here for database searches, BLAST etc.)
- EcoSal Plus (ASM Book on E. coli, Salmonella and enterics)
- EDGAR II (Experimental Design Generator And Rndomiser)
- EMBL (The European Molecular Biology Laboratory)
- EnsemblBacteria Over 30,000 genome sequences from bacteria and archaea have been annotated and deposited
- Entrez – National Center for Biotechnology Information
- ExPASy
- Google Scholar
- Gecoviz: A tool you may find interesting to see whether the genomic context of your genes is conserved across bacteria.
- 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)
- In silico simulation of molecular biology experiments
- KEGG (Kyoto Encyclopedia of Genes and Genomes. Find ezymes and cross-links from all the genome projects)
- MG-RAST metagenomics analysis server
- MicrobesOnline (great tool for genome comparison and gene analysis)
- Microbes Info (Under construction)
- Multiple Sequence Alignment (Clustal Omega)
- NCBI (National Center for Biotechnology Information)
- NDB Nucleic Acid Database – A Portal for Three-dimensional Structural Information about Nucleic Acids
- Plant Metabolic Network
- PubMed (NCBI)
- RSAT Regulatory Sequence Analysis Tools
- RhizoDB
- Rlv3841 annotation (Latest annotation as an Excel spreadsheet)
- RNA secondary structure prediction (eg stem loops)
- SalisLab RBS Calculator
- Salmonella Genetic Stock Centre (SGSC)
- Sinorhizobium meliloti website (Turlough’s site)
- STRING – Known and Predicted Protein-Protein Interactions
- TMHMM Server; Prediction of transmembrane helices in proteins
- TransportDB – Genomic Comparisons of Membrane Transport Systems (Paulson’s site)
- UniProtKB/Swiss-Prot
- Wellcome Trust Sanger Institute
Rhizosphere 