EMOPEC

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{[ r.upstream.substr(10) ]}{[ r.sd ]}{[ r.spacing ]} {[ r.cds.substr(0, 3) ]}{[ r.cds.substr(3, 17) ]} ({[ (r.expression_percent * 100).toFixed(1) ]}%)
{[ oligo[1].substr(0, 42) ]}{[ oligo[1].substr(42, 6) ]}{[ oligo[1].substr(48) ]} {[ (oligo[2] * 100).toFixed(1) ]}% {[ oligo[3].toFixed(1) ]} kcal/mol

Options

Target
Whether the library is up- or down-regulating or both.
Spacing
How many nucleotides between start codon and Shine-Dalgarno sequence.
Size
Number of oligos to generate.
Constraints
Use IUPAC degenerate base symbols (A,T, .. N) to put constraints on the designed library. The constraints sequence will be right-aligned to the initiation codon, it is therefore not necessary to input the full length of the leader sequence.

Oligo Libraries

EMOPEC can be used to create libraries of oligos for recombineering. Enter a library size, and select the library type. "both" will ignore wt sequence expression and select a library from minimal expression to maximum expression. "up" or "down" will create a library starting from predicted wt expression level and target maximum or minimum expression levels. All libraries are created in a linear fashion. Click [show library] to show the created library displaying the oligo, predicted expression level and the alteration in secondary structure energy (ΔΔGmRNA).

Expression values

Expression values are normalized as a percentage of the fluorescence of the highest scoring SD sequence in the EMOPEC dataset (AGGAGA).

Notes on spacing

The spacing input is based on the number of nucleotides between the Shine-Dalgarno sequence and the start-codon. This spacing will be one nucleotide longer than the spacing used by other tools, such as the RBS Calculator and UTR Designer, which uses the longer ribosome recognition site (RRS) instead of the SD sequence.