Dataset Information

Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping.

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.

SUBMITTER: Orenstein Y

PROVIDER: S-EPMC5661997 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping.

Orenstein Yaron Y Puccinelli Robert R Kim Ryan R Fordyce Polly P Berger Bonnie B

Cell systems 20170901 3

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 w ...[more]

PMID: 28957657

Similar Datasets

Project description:PurposeAdvanced diffusion magnetic resonance imaging benefits from collecting as much data as is feasible but is highly sensitive to subject motion and the risk of data loss increases with longer acquisition times. Our purpose was to create a maximally time-efficient and flexible diffusion acquisition capability with built-in robustness to partially acquired or interrupted scans. Our framework has been developed for the developing Human Connectome Project, but different application domains are equally possible.MethodsComplete flexibility in the sampling of diffusion space combined with free choice of phase-encode-direction and the temporal ordering of the sampling scheme was developed taking into account motion robustness, internal consistency, and hardware limits. A split-diffusion-gradient preparation, multiband acceleration, and a restart capacity were added.ResultsThe framework was used to explore different parameters choices for the desired high angular resolution diffusion imaging diffusion sampling. For the developing Human Connectome Project, a high-angular resolution, maximally time-efficient (20 min) multishell protocol with 300 diffusion-weighted volumes was acquired in >400 neonates. An optimal design of a high-resolution (1.2 × 1.2 mm2 ) two-shell acquisition with 54 diffusion weighted volumes was obtained using a split-gradient design.ConclusionThe presented framework provides flexibility to generate time-efficient and motion-robust diffusion magnetic resonance imaging acquisitions taking into account hardware constraints that might otherwise result in sub-optimal choices. Magn Reson Med 79:1276-1292, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Dataset Information

Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping.

Publications

Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets