Team:Imperial College/DISC
VESICLES was born out of the pure monotony of ensuring DNA sequences are correct before sending them off for synthesis. DNA synthesis is an important part of synthetic biology, and any errors in the sequences that are synthesized can be detrimental to the success of any iGEM team. One wrong base can put an end to a project.
When compiling sequences for a parts list from literature sources as well as the iGEM Registry, whitespace, uncapitalized bases and invalid (ie. not A, T, C, G) characters may be accidentally included as well. The key function of this software is to filter out these errors from sequences and add corrected sequences to a DNA parts list, ensuring synthesis of the correct DNA parts. This software is also capable of checking sequences against this list to ensure no duplicates are added, or whether sequencing results do in fact match up to the DNA sequences on the parts list.
To download VESICLES, click HERE!
Alternatively, you can find VESICLES on Github HERE!
Walkthrough Documentation
To add DNA sequences to the parts list:
Open the VESICLES-master folder. Double-click and open save2partslist.R with RStudio. Run the script. In Rstudio, using the keyboard shortcut CTRL+ALT+R does this. Alternatively you can click through the menu bar.
Next, at the bottom of the R Console, type: save2partslist("the part's name","the sequence"). The sequence can be copied and pasted in, but please note the quotation marks must be included. Now hit enter:
All whitespace will be removed from the sequence, and all lowercase letters will be capitalized before it is added into a file in VESICLES-master called partslist.txt
NOTE: The partslist.txt file will be created if none already exists in the VESICLES-master folder. Otherwise, new entries will be added to this file.
Additionally, you will not be able to add parts to this list if invalid DNA characters are contained in the sequence (ie. anything other than A, T, C, G). You will be notified in the R console if the sequence contains invalid characters.
Also, you will not be able to add parts with duplicate names or sequences to anything on the list. If the whitespace-removed, fully capitalized version of a messy sequence you attempt to add to the parts list matches a DNA sequence already entered into it, you will be notified of this in the R console and of which part your new attempted entry is a duplicate of. You will also be notified if the name for the part you are trying to enter is a duplicate of a name already in the list. These features can also be used to check sequences against your DNA parts on the list to see if they match.
NEVER EDIT PARTSLIST.TXT USING A TEXT EDITOR. THIS MAY PREVENT YOU FROM SUBSEQUENTLY ADDING NEW PARTS TO THE LIST. SEE BELOW FOR HOW TO REMOVE PARTS.
NEVER EDIT PARTSLIST.TXT USING A TEXT EDITOR. THIS MAY PREVENT YOU FROM SUBSEQUENTLY ADDING NEW PARTS TO THE LIST. SEE BELOW FOR HOW TO REMOVE PARTS.
If your partslist.txt file contains only 1 entry, just delete the file.
If there is more than 1 entry in partslist.txt, to remove DNA parts from the parts list:
Open the VESICLES-master folder. Make sure the partslist.txt file that you want to remove parts from is in the folder. Double-click and open deleteLotsOfPartsFromList.R with RStudio. Run the script. In Rstudio, using the keyboard shortcut CTRL+ALT+R does this. Alternatively you can click through the menu bar.
Next, at the bottom of the R Console for as many parts as you want to delete, type: deleteLotsOfPartsFromList("part name 1", "part name 2", "part name 3",...). Please note the quotation marks must be included. Now hit enter:
The part names and their sequences will be removed from partslist.txt:
You will be notified in the R console window if the part was successfully deleted from the list or if your attempt to delete anything was unsuccessful.
