is an extant relative of the earliest terrestrial plants and has attracted a substantial interest as a model organism for evolutionary and developmental studies. Given its relatively simple genome, compact gene families, simple morphology, ease of propagation and transformation, is becoming a promising platform for plant synthetic biology. Modular genetic parts have been essential for development of synthetic biology approaches, so we sought to design an engineering oriented database for genetic parts where each gene is a standalone functional unit. MarpoDB is a database of genes and genetic parts, which is tailored to become an integral tool for a synthetic biology workflow. Among its features are precompiled cross-database querying to InterPro, Pfam signatures and non-redundant BLAST annotations; BLAST querying to genes; sequence export in GenBank format; recoding of sequences to the common syntax for type IIS assembly and exchange of DNA parts; and a minimalistic, intuitive and interactive user interface for gene models and sequence exploration. Furthermore, we have implemented user input to encourage feedback, collaboration and exchange between the MarpoDB community. MarpoDB source-code is released on GitHub to promote development of computational tools for synthetic biology.
Biotechnology and Biological Sciences Research Council (BB/L014130/1)
This work was supported by the Chilean Comisión Nacional de Investigación Científica y Tecnológica (CONICYT) [Becas Chile and Cambridge Trust joint Scholarship to B.P.]; the Biotechnology and Biological Sciences Research Council and Engineering and Physical Sciences Research Council Synthetic Biology Research Centre supported by the Research Councils’ Synthetic Biology for Growth Programme [OpenPlant grant No. BB/L014130/1 to J.H.]; and University of Cambridge BBSRC DTP programme [M.D.]