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RBS Library Calculator
Title


Genomic RBS Sequence [?]
Ribosome Binding Site Sequence: enter an initial ribosome binding site sequence, using A/G/C/T/U. A complete RBS sequence is 35 nucleotides long. If none is selected, a random one will be generated and used as the initial condition.
Genomic Protein CDS [?]
Protein Coding Sequence: enter a nucleotide sequence (at least 50 bp) that encodes a protein, using A/G/C/T/U. Begins with a start codon (ATG/GTG/TTG/CTG). (required)
 
Max Length of Mutation Box [?]
Maximum Number of Consecutive Degenerate Nucleotides: The number of consecutive mutations to the genome partly determine the efficiency of genome editing via oligo-mediated allelic recombinant (OMAR) or MAGE. Select the maximum number of consecutive nucleotides that may be mutated, compared to the initial RBS sequence. Typical values are from 4 to 20 nucleotides.
RBS Constraints [?]
Ribosome Binding Site Sequence Constraints: enter a degenerate nucleotide sequence that determines which mutations to the RBS are allowable. Insert a N where mutations are desired or A/G/C/T/U where mutations are not desired. (required)
(optional)


Minimum Translation Initiation Rate [?]
RBS Library's Minimum Translation Initiation Rate: select the desired minimum rate of translation initiation within the optimized ribosome binding site library, on a proportional scale from 0.1 to 100,000 or more. This will determine the lowest protein expression level within the library. (required)
Maximum Translation Initiation Rate [?]
RBS Library's Maximum Translation Initiation Rate: select the desired maximum rate of translation initiation within the optimized ribosome binding site library, on a proportional scale from 0.1 to 100,000 or more. This will determine the highest protein expression level within the library. (required)


Target Library Size: 16     Low Res    
    High Res
Organism or (16S rRNA) [?]
Organism or 16S rRNA sequence: choose a bacterial species by typing in the first 3 letters of its name and selecting it from the list. Alternatively, you may enter the last 9 nucleotides of the 16S rRNA, using A/G/C/T/U. (required)
(start typing)


Design Jobs: 2 queued, 3 currently running
When using these results, please reference: Iman Farasat, Manish Kushwaha, Jason Collens, Michael Easterbrook, Matthew Guido, and Howard M. Salis, "Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria", Molecular Systems Biology, v10(6), 2014
Method online since January 10th, 2011.
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We gratefully acknowledge research funding from the Defense Advanced Research Projects Agency, the National Science Foundation, the Office of Naval Research, and an Amazon AWS Research Grant.
Computational resources are provided by the AWS Elastic Compute Cloud.