Software

BBrickIt is a software that BioBricks any DNA sequence for you. According to the BioBrick standards, each BioBrick part must have a Prefix and Suffix. In order for a part to be compatible with BioBrick RFC[10] standards, it must not contain the following restriction sites, as these are unique to the prefix and suffix:

Sequence Type Enzyme
gaattc Illegal EcoRIt
tctaga Illegal XbaI
actagt Illegal SpeI
ctgcag Illegal PstI
gcggccgc Avoid NotI

If the sequence to be contains any of these sites, the program will detect them and they will be highlighted. The software will also suggest another sequence, with the illegal sequences replaced by new sequences which do not change the overall amino acid coding sequence. The most exciting feature of this application is that it takes into account the codon preferences for your chassis organisms. The frequency and efficiency of usage of codons in different organisms are different for producing the same amino acid. BBrickIt takes that into account and then suggests a new sequence that is optimized for the chassis organism.

BBrickIt v.2 builds upon the previous version of BBrickIt. This previous version of BBrickIt has been completely developed by our own ICT Mumbai iGEM Team of 2018. We have modified it this year. Users can now input an mRNA sequence in the input field and the software will convert it to the corresponding DNA sequence and return the BioBrick. It also comes with a “Copy BioBrick Sequence” button to enable users to copy the BioBrick sequence to their clipboard with the click of a button. Several bug fixes have also been made.

Steps to Use BBrickIt:

  1. Select your Organism/Chassis.
  2. Paste your sequence in the box at the top.
  3. Choose if your sequence is a coding sequence or not.
  4. Click BioBrick!
  5. If you wish to take the reverse complement of the sequence and then BioBrick it, click If your part contains any illegal restriction enzyme binding sites, two boxes will appear. The box on the left will display the highlighted restriction sites with a legend at the bottom. The box on the right will suggest the new, optimized sequence for the selected organism. If you wish to proceed with that sequence, copy and paste it into the top box and hit BioBrick.


Pareto Plot

You can find the source code and executable file here.