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RedLibs Sequence Generator RedLibs (standalone)
Input
RedLibs
Enter sequences and numerical values
(e.g. 5’-UTRs and rTRs)
or
Upload a file
RedLibs (standalone) is a tool that generates sequence libraries that follow a uniform distribution for a user-specified numerical sequence parameter while being encoded by individual degenerate sequences for facile cloning. These libraries have a user-defined size (i.e. number sequence variants encoded by the degenerate sequence).
Input
In the first window, the user can specify a list of sequence-value pairs. Either the query window (one sequence per row) or file upload (*.txt files) may be used. Note that any type of DNA/RNA sequences are accepted as long as they have the same length.
Example:
AGAAAAAAATAATTGGA,0.05807638
AGAAAAACATAATTGGA,0.055958934
AGAAAAAGATAATTGGA,0.12676555
AGAAAAATATAATTGGA,0.05761717
AGAAAACAATAATTGGA,0.048265565
AGAAAACCATAATTGGA,0.049254492
…
In the second window, different target parameters for the library optimization can be specified, most importantly, the desired target size (see mouseovers for explanations of the other parameters).
Output
The output of RedLibs (standalone) comprises a comma-separated list of the TopX (default: Top10) optimized libraries (*.txt) as well as a graphical output thereof (*.png). The *.txt file specifies the degenerate sequences of the libraries, as well as the sequences of individual library members and their numerical parameter value (“strength”). The *.png file displays histograms for the TopX libraries that visualize the distribution of the numerical parameter and the uniformity for each library.

When you use the RedLibs in your published work, please do not forget to cite:

  • Jeschek, M., Gerngross, D., & Panke, S. (2016). Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort. Nature communications, 7, 11163 (https://doi.org/10.1038/ncomms11163)

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