20 Mapping sequences to parts After starting a DeviceEditor session, it is possible to map a sequence to a new part. Demonstration video: Here is a demonstration video that goes through this process (Create and map new part.mov, right click this link to save the movie to disk for better viewing): Here is a DeviceEditor .xml saved design file resulting from saving after the demonstration above (Create and map new part.xml, right click and save link as to save the design file to disk): Narrative: Each column/row location in the collection may be associated with a part. Mapping a sequence to a part: We have several options for mapping a sequence a part: either from a local Genbank format sequence file or from a sequence that has been copied to the clipboard (i.e. a copy/paste like operation from either a plain-text DNA sequence, or from Vector Editor (part of the JBEI-ICE Repository platform)). Note: when mapping a sequence from an ICE-tethered VectorEditor, a link back to the sequence entry in ICE will be displayed in the part info tab. Right-clicking on a column/row location in the collection will provide options to map from a Genbank file, or from the clipboard. Mapping from a Genbank sequence file: Selecting "Map from Genbank" will bring up a "Select file to upload" dialog box for specifying the Genbank format sequence file you would like to map sequence information from. In this particular example, we'll right click the first row in the first column of the collection, and we'll be mapping from the file pBbB2a_GFP.gb (right click and save link as to save to disk): With the file pBbB2a_GFP.gb selected, a new "Specify Part Definition" dialog box will pop-up that will allow us to specify the part definition. The first thing we will want to do is to give our part a name, in this case we'll call it "BBR1-ori". Note that the part source is automatically grabbed from the LOCUS line of the Genbank file ("pBbB2a-GFP" in this example). Next, we will indicate that we don't want to use the entire sequence in this Genbank file for our part. Instead, we will select "Specified Sequence" from the pull-down menu next to "Sequence" in the dialog box. The start bp for the BBR1-ori is 1618 and the end bp is 2908 (since the "BBR1-ori" feature is annotated in this Genbank file, you can find these start/end bp numbers in the "Source Data" display portion of the dialog box, which contains the text contents of the Genbank file), and we will enter these numbers accordingly in the StartBP and StopBP fields of the dialog box. Also note that the "BBR1-ori" feature is located on the complement strand, so we will also click the "Reverse Complement" check box in the dialog box. Finally, we click the "Done" button, to finish mapping the sequence information to the part. Mapping from a FASTA sequence file: See the mapping from the clipboard (plain-text) section below. Mapping from the clipboard (from a VectorEditor copy to clipboard): In this particular example, we'll be mapping from the file pBbE5a_GFP.gb (right click and save link as to save to disk): To map a sequence to a part from the clipboard follows a very similar procedure. In this example, we'll right-click on the first row in the second column of the collection. This time we will select "Map from Clipboard". A new dialog box will pop-up, instructing us to right-click paste into the box below. For this particular example, we will copy the GFP feature from the plasmid pBbE5a-GFP in VectorEditor. We'll change tabs in our browser to a Vector Editor session with the pBbE5a-GFP sequence open. We'll click the GFP feature to select it, and right-click to "Copy". Then, we'll change browser tabs back to our DeviceEditor session, and right-click paste the copied GFP feature in the dialog box. After doing this, a new "Specify Part Definition" dialog box will pop-up, similar to that seen above when we were mapping from a Genbank file, except that the "StartBP" and "StopBP" fields (in this example 1615 and 2331, respectively) have been pre-filled to correspond with the highlighted portion (GFP feature) of the pBbE5a-GFP sequence we were pasting from. To details on how this is implemented, see the DeviceEditor system clipboard interface specification section. The first thing we will want to do is to give our part a name, in this case we'll call it "GFP". As above when mapping from a Genbank file, the name of the source of our part ("pBbE5a-GFP") is already pre-filled. Note that when pasting from VectorEditor, the entire sequence context of the part is also pasted into DeviceEditor (very useful for downstream DNA assembly design using j5). Note also that you will still need to specify if the part you are defining (in this case the GFP ORF) lies on the complement strand or not (in this example, it does not, so we will leave the "Reverse Complement" box unchecked). We again click "Done" to finish mapping the sequence information to the part. Note: as stated above, when mapping a sequence from an ICE-tethered VectorEditor, a link back to the sequence entry in ICE will be displayed in the part info tab. Mapping from the clipboard (from a plain-text copy to clipboard): If, instead of copying the sequence information from VectorEditor (which also carries along with it meta-data), we were to copy from a plain-text DNA sequence (no meta-data), we'd follow a similar procedure. In this example, we'll right-click on the first row in the third column of the collection. We will again select "Map from Clipboard". A new dialog box will pop-up, instructing us to right-click paste into the box below. For this particular example, with a text editor (e.g. Notepad or TextEdit), we will open a text file (pBbS8c-RFP.fas, see below) that contains the DNA sequence of pBbS8c-RFP (which happens to be in FASTA format), and copy the contents of entire plasmid sequence to the clipboard (highlighting and then copying DNA sequence from within plasmid editor programs, such as VectorNTI, ApE or GENtle, to the clipboard also works). Returning to the DeviceEditor tab in our browser, we'll right-click paste the copied plain-text sequence into the dialog box. After doing this, a new "Specify Part Definition" dialog box will pop-up, similar to that seen above. The first thing we will want to do is to give our part a name, in this case we'll call it "dblterm". Then, we'll want to given the source of our part ("pBbS8c-RFP") a name. The "StartBP" and "StopBP" fields default to the first and last bps of the plain-text sequence we pasting in (in this example 1 and 5213, respectively). We'll change these to 1948 and 2076, to coincide with just the double terminator portion of the sequence. Note what we did here, namely when mapping from the clipboard from plain-text, in order to capture the entire sequence context of the part pasted into DeviceEditor (which is very useful for downstream DNA assembly design using j5), you will need to paste in the entire (plasmid) sequence containing the part, and then specify the "StartBP" and "StopBP" fields to correspond with the boundaries of the part (as was done above when mapping from a Genbank file). Note also that you will need to specify if the part you are defining (in this case the double terminator) lies on the complement strand or not (in this example, it does not, so we will leave the "Reverse Complement" box unchecked). We again click "Done" to finish mapping the sequence information to the part. Here is the text file (pBbS8c-RFP.fas) that contains the plain-text DNA sequence of a double terminator part (right click and save link as to save to disk): Important note when mixing the above mapping methods for the same sequence file: It is possible to repeatedly map (various sub-sections of) the same sequence file to multiple parts. For example, an alternate way to accomplish the example above would have been to grab both the BBR-ori and the GFP sequence features from the same plasmid pBbB2a-GFP. This works well if using the same mapping method (e.g. map from Genbank, map from VectorEditor clipboard, map from plain-text clipboard) consistently for the same sequence file. However, if you use multiple mapping methods for the same sequence (e.g. first map from Genbank, and then map from VectorEditor clipboard), DeviceEditor will issue a warning message (e.g. "Another file with the Display ID pBbB2a_GFP already exists.  Please ensure the Display ID is unique and try again.") because it thinks that you using the same name for two distinct sequence files. To avoid this problem, simply use one mapping method consistently. The map from (VectorEditor) clipboard method is preferred in this situation. Resulting mapped part icons: Note that the borders of our mapped parts have become a darker grey (from either light grey, or from red if the parts had names but had yet to be mapped to a sequence), indicating that we have mapped sequences to them. With a part selected in the design canvas (highlighted in a light blue), the "Part Info" tab in the right panel of the display will be active, and the part information will be displayed therein. After mapping a sequence to a part, it is possible to change a part's name or definition, change the assembly strategy for a part, create Eugene design specification rules for the part, and copy/paste the part (between DeviceEditor sessions).