Biomedical Engineering Reference
In-Depth Information
tools. Online user's manuals provide additional documentation
and specifi c demonstrations of how to use j5 [
53
], DeviceEditor
[
59
], and PR-PR [
50
]. The published j5 [
17
], DeviceEditor [
18
],
VectorEditor [
19
], and PR-PR [
20
] research articles (along with
their supplemental materials) provide further information includ-
ing algorithm and software implementation details. The methods
described in this chapter apply specifically to j5 v2.3.6,
DeviceEditor v2.1.1, VectorEditor v1.7.3, and PR-PR v1.1.
While it is anticipated that these software tools will continue to be
developed and that their interfaces and functionalities may diverge
from what is described here, the overall workfl ow for these tools
is not anticipated to change signifi cantly in the short term. That
said, referring to their online user's manuals (cited immediately
above) is the best means to ensuring up-to-date information.
3. Mapping GenBank Files to Parts in DeviceEditor. Mapping
annotated DNA sequences to parts in DeviceEditor from
VectorEditor via the system clipboard (Subheading
3.5
) is gener-
ally preferred over mapping directly from GenBank sequence
fi les. Several DNA software tools (such as Sci-Ed Central's Clone
Manager software) do not export properly formatted GenBank
sequence fi les. While VectorEditor is able to successfully parse
many of these nonstandard GenBank-like sequence fi les, j5 may
not be able to. Passaging DNA sequence information through
VectorEditor mitigates the downstream risk of j5 failure due to
incorrectly formatted GenBank sequence fi les. Some DNA
software tools (e.g., VectorNTI, ApE [
60
]) export GenBank
sequence fi les which in general are successfully parsed by j5. Since
some users may prefer to map annotated DNA sequences directly
from GenBank sequence fi les, it is important to briefl y describe
how this is accomplished. To map an annotated DNA sequence
directly from a GenBank fi le to a part in DeviceEditor, right-click
the desired part and select “Map from Genbank.” A Select File to
Upload dialog box will open. Select the desired GenBank
sequence fi le. A “Specify Part Defi nition” dialog box will open,
which will display the “Part Name,” the “Part Source” (the
“LOCUS” fi eld in the GenBank fi le), and the “Source Data”
(the contents of the GenBank fi le including all sequence annota-
tion information). As described in Subheading
3.5
, DeviceEditor
does not allow distinct GenBank sequence fi les with the same
sequence name (i.e., “LOCUS” fi eld) to be sequentially mapped
to parts. As such, it may be necessary to rename the various
sequences (not the fi le names, but rather the “LOCUS” fi elds) in
order to make the name of each distinct sequence unique. Either
the “Whole Sequence” or a “Specifi ed Sequence” (spanning
from “StartBP” to “StopBP”) can be mapped to the part. If the
reverse complement of the selected sequence is to be mapped to
the part, click to activate the “Reverse Complement” check-box.
Click the “Done” button, concluding the mapping process.
