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R2oDNA Designer

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.

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1 user review

1 user review

Hailong Li's avatar image Hailong Li's country flag

Hailong Li

This is a very good web software for your sequence design. Fantastic work! Previously I saved it for limited to around 16mer orthogonal sequence design. Now it's updated to neutral and up to 200mer bases. Great! I would like to save it as a standalone software and hope it can be maintained forever.

R2oDNA Designer forum

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R2oDNA Designer classification

R2oDNA Designer specifications

Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable

R2oDNA Designer distribution

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R2oDNA Designer forum

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No open topic.

R2oDNA Designer classification

R2oDNA Designer specifications

Interface:
Web user interface
Computer skills:
Basic
Maintained:
Yes
Restrictions to use:
None
Stability:
Stable

R2oDNA Designer support

Maintainer

  • James T. MacDold <>
  • James T. MacDold <>

Credits

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Publications

Institution(s)

Imperial College London, London, UK

Link to literature

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