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Related Experiment Video

Updated: Feb 22, 2026

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping.

Yaron Orenstein¹, Robert Puccinelli², Ryan Kim³

¹Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

|September 29, 2017

Summary

This summary is machine-generated.

This study introduces JokerCAKE, an algorithm that uses joker characters to create smaller sequence libraries for DNA-protein binding experiments. This enables broader sequence space exploration with fewer resources.

Keywords:

de Bruijn graph microarray design sequence libraries

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Area of Science:

Bioinformatics
Computational Biology
Molecular Biology

Background:

Measuring binding affinities of oligonucleotides and peptides requires comprehensive k-mer libraries.
The exponential growth of k-mers with increasing k limits experimental space and increases costs.

Purpose of the Study:

To develop a computationally efficient algorithm for generating reduced-size k-mer libraries.
To enable broader exploration of sequence space in binding experiments without increasing experimental costs.

Main Methods:

Developed the JokerCAKE algorithm to generate sequences containing joker characters.
Each k-mer appears at least p times with at most one joker character per k-mer.
Validated JokerCAKE library performance against existing data and new experimental results.

Main Results:

JokerCAKE algorithm produces near-optimal, reduced-size k-mer libraries.
Accurate binding scores for high-affinity k-mers can be inferred from JokerCAKE libraries.
Demonstrated significant expansion of searchable sequence space for the same experimental cost.

Conclusions:

JokerCAKE offers a cost-effective method for universal and unbiased binding measurements.
Enables researchers to investigate a larger sequence space with existing experimental platforms.
Facilitates more comprehensive studies of molecular interactions.