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. 2010 May;38(8):2603-6.
doi: 10.1093/nar/gkq143. Epub 2010 Mar 8.

GeneDesign 3.0 is an updated synthetic biology toolkit

Sarah M Richardson  1 , Paul W Nunley, Robert M Yarrington, Jef D Boeke, Joel S Bader
Affiliations

GeneDesign 3.0 is an updated synthetic biology toolkit

Sarah M Richardson et al. Nucleic Acids Res. 2010 May.

Abstract

GeneDesign is a set of web applications that provides public access to a nucleotide manipulation pipeline for synthetic biology. The server is public and freely accessible, and the source is available for download under the New BSD License. Since GeneDesign was published and made publicly available 3 years ago, we have made its code base more efficient, added several algorithms and modules, updated the restriction enzyme library, added batch processing capabilities, and added several command line modules, all of which we briefly describe here.

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Figures

Figure 1.
Figure 1.
Visits to GeneDesign in a 6-month period have come from 368 cities in 47 countries, as measured by Google Analytics. The diameter of the circle corresponds to number of visits.
Figure 2.
Figure 2.
Distribution of visiting network types to GeneDesign in a 6-month period, as measured by Google Analytics.
Figure 3.
Figure 3.
Distribution of access to GeneDesign modules in a 6-month period, as measured by Google Analytics.
Figure 4.
Figure 4.
Output from the codon bias graphing module visualizing the average RSCU value across the wild-type and optimized sequences for the integrase/reverse transcriptase polyprotein from yeast Ty1. The boundary between the two protein coding regions can be seen in the wild-type curve as a deep valley at offset 600; the optimized curve does not have this valley.
See this image and copyright information in PMC

References

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