Ask Nicole, Amanda, or Janet for the lab log-in.SBOL (synthetic biology open language) visual format.Sabio-RK: biochemical reaction kinetics database.intermediate level: AMAZING Cheat Sheet.Quickie PyMol Tutorial: great script syntax examples.NuPack Nucleic acid secondary structure predictor.Finnzyme multiple primer analyzer looks for primer dimers (check before ordering primers).Finnzyme Tm calculator: use if you use Phusion DNA polymerase.Check your forward engineering designs with more bp included in the reverse engineering mode. Pretty sensitive to the amount of upstream & downstream sequence info you provide. There is a 47% chance that a synthetic ribosome binding site will be accurate to within 2-fold of its predicted translation initiation rate." So you can estimate it to have accuracy within an order of magnitude. Accuracy stated by FAQ: "on average, the predictions of the RBS Calculator are accurate to within a factor of 2.3, equivalent to an error of 1.82 kcal/mol in the thermodynamic model.RBS strength calculator/engineering tool.Conservative substitutions, as judged by the substitution matrix, are indicated with +." If the query and the subject have the same amino acid at a given location, the residue itself is shown. protein alignments: "The line between the two sequences indicates the similarities between the sequences.The most commonly used nucleotide/protein alignment tool.Class II genes correspond to genes highly and continuously expressed during exponential growth. Class I contains genes involved in most metabolic processes.from HÉNAUT and DANCHIN:Analysis and Predictions from Escherichia coli sequences.Requires more selections, so is less simple than the IDT one.(Boo!) However, IDT is a leading company for DNA technology, so whatever they use is likely fine. Doesn't provide any info about the strategy used for codon optimization.IDT's web tool to optimize for a given organism.Plasmid figures may be rendered in PNG, JPG, SVG or SVGZ format. The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input.Serial Cloner free equivalent to Vector NTI.NEB Molecular Cloning Technical Guide: overview and comparison of most types of cloning.Molecular Biology DNA/RNA Tools Cloning guides EcoSal !!subscription required!! (not available at UW). The Polymerase Chain Reaction, Gel Electrophoresis, Restriction Endonucleases, DNA Sequencing, Antisense Technologies, A Basic PCR Protocol.Mitochondrial DNA, Mendelian Genetics, Molecular Facts and Figures, Protein Synthesis, microRNAs, DNA Replication, A Brief History of DNA, What is an Oligo.general biology/biotech basics from Integrated DNA Technologies (IDT).
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