ArticlePloS one2017
Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- The design and engineering of synthetic genomes.Nature reviews. Genetics · 2025Review
- BAC-browser: the tool for synthetic biology.BMC bioinformatics · 2025Article
- Investigation of Genome Biology by Synthetic Genome Engineering.Bioengineering (Basel, Switzerland) · 2023Review
- Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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Authors and funding
4 authors.
Funding
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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 designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.
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