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A web application that stochastically generates orthogonal sets of synthetic DNA sequences designed to be biologically neutral. Biologically neutral sequences may be used for directing efficient DNA assembly by overlap-directed methods, as a negative control for functional DNA, as barcodes, or potentially as spacer regions to insulate biological parts from local context. The software creates optimized sequences using a Monte Carlo simulated annealing approach followed by the elimination of sequences homologous to host genomes and commonly used biological parts. An orthogonal set is finally determined by using a network elimination algorithm. Design constraints can be defined using either a web-based graphical user interface (GUI) or uploading a file containing a set of text commands. Web based graphical interface (GUI) is commonly used in Microsoft Windows, Mac OS, media players, smartphones, kasinot ilman rekisteröitymistä gaming devices and many other electronic devices.

Specifications

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
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Interface:
Web user interface
Restrictions to use:
None
Computer skills:
Basic
Stability:
Stable
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Documentation & support

Maintainer

  • James T. MacDonald <j.macdonald at imperial.ac.uk>

Credits

Institution(s)

Imperial College London, London SW7 2AZ, United Kingdom

Publications

  • (Casini et al., 2014) R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences. ACS synthetic biology. PMID: 24933158

Classification

Literature

  • (Ellis et al., 2011) DNA assembly for synthetic biology: from parts to pathways and beyond. Integrative biology. PMID: 21246151

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