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• W2760148613 abstract "Sequence libraries that cover all k-mers enable universal, unbiased measurements of binding to both oligonucleotides and peptides. While the number of k-mers grows exponentially in k, space on all experimental platforms is limited. Here, we shrink k-mer library sizes by using joker characters, which represent all characters in the alphabet simultaneously. We present the JokerCAKE (joker covering all k-mers) algorithm for generating a short sequence such that each k-mer appears at least p times with at most one joker character per k-mer. By running our algorithm on a range of parameters and alphabets, we show that JokerCAKE produces near-optimal sequences. Moreover, through comparison with data from hundreds of DNA-protein binding experiments and with new experimental results for both standard and JokerCAKE libraries, we establish that accurate binding scores can be inferred for high-affinity k-mers using JokerCAKE libraries. JokerCAKE libraries allow researchers to search a significantly larger sequence space using the same number of experimental measurements and at the same cost." @default.
• W2760148613 created "2017-10-06" @default.
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• W2760148613 date "2017-09-01" @default.
• W2760148613 modified "2023-09-24" @default.
• W2760148613 title "Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping" @default.
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• W2760148613 doi "https://doi.org/10.1016/j.cels.2017.07.006" @default.
• W2760148613 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/5661997" @default.
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• W2760148613 hasPublicationYear "2017" @default.
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