Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications

PloS One
Matthias ChristenBeat Christen

Abstract

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA ...Continue Reading

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Citations

Apr 3, 2019·Proceedings of the National Academy of Sciences of the United States of America·Jonathan E VenetzBeat Christen

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Datasets Mentioned

BETA
NA1000

Methods Mentioned

BETA
PCR
electrophoresis
PCRs

Software Mentioned

Genome Calligrapher
Genome Partitioner
Genome
GenomeCalligrapher
Bio
GenomeDiagram
BioBricks
Biopython
BASIC
RNAseq

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