Biomedical Engineering Reference
In-Depth Information
4. Alternative Methods for Creating Input Files for j5. In addition
to DeviceEditor, there are alternative means to creating input
fi les for j5. When designing a DNA assembly protocol, j5 takes
as input a set of fi les that specify the order and sequences of the
DNA fragments that are to be assembled. A zipped collection
of DNA sequence fi les provides the annotated sequences of the
DNA fragments. CSV fi les specify which of the zipped DNA
sequence fi les to input; the locations of the DNA fragments
within the DNA sequences; the order in which to assemble the
DNA fragments; the user's collections of plasmids, DNA oli-
gos, and synthesized DNA fragments; and the parameters (e.g.,
the cost of DNA synthesis) that tailor the protocol design pro-
cess. A plain-text Eugene design specifi cations rule fi le [
54
,
55
]
specifi es rules that constrain undesirable DNA part combina-
tions from being constructed (e.g., prevent plasmids with more
than one copy of a particular terminator sequence). Aside from
DeviceEditor and VectorEditor, various DNA software (e.g.,
VectorNTI, ApE) can be used to prepare the annotated DNA
sequences; spreadsheet software (e.g., Excel, OpenOffi ce) can
be used to prepare the CSV fi les; and text editor software (e.g.,
Notepad, TextEdit) can be used to prepare the Eugene design
specifi cations rule fi le. Manually prepared j5 input fi les can be
either imported into DeviceEditor (
see
Subheadings
3.3
and
3.7
) or submitted to j5 via the aforementioned simplifi ed web-
form or XML-RPC web-service interfaces.
Acknowledgments
Confl ict of Interest Statement
: The author declares competing
fi nancial interests in the form of pending patent applications related
to the j5 software, and equity in TeselaGen Biotechnology, Inc.
This work conducted by the Joint BioEnergy Institute and the
U.S. Department of Energy Joint Genome Institute was supported
by the Offi ce of Science, Offi ce of Biological and Environmental
Research, of the U.S. Department of Energy under Contract No.
DE-AC02-05CH11231. The author thanks Joanna Chen for con-
structive comments on the manuscript.
References
1. Ellis T, Adie T, Baldwin GS (2011) DNA
assembly for synthetic biology: from parts to
pathways and beyond. Integr Biol (Camb)
3:109-118. doi:
10.1039/c0ib00070a
2. Hillson NJ (2011) DNA assembly method
standardization for synthetic biomolecular cir-
cuits and systems. In: Koeppl H, Densmore D,
di Bernardo M, Setti G (eds) Design and analy-
sis of bio-molecular circuits, 1st edn. Springer,
New York, pp 295-314
3. Densmore D, Hsiau TH, Kittleson JT et al
(2010) Algorithms for automated DNA assem-
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