Team:SUSTC-Shenzhen-B/achievements

Achievements

Software

1. If users input the full sequence of terminator, our program can divide it into three parts, A tail, stemloop, and T tail.

2. By using Free energy(or Hairpin Score) Minimization Rule, we can get secondary structure of stemloop. Then we can output a picture of the terminator.

3. By using the efficiency data from lecture, database and a few our experiment results,we determined the parameters of our algorithm. However, because of the time limit, we have not finished to measure more than one hundred terminators to get the best fitting equation between score and terminator efficiency. So our future software version will perform better.

Database

To build a complete rho-independent terminator system, we had to create a new terminator efficiency database which can make users choose the terminator they need more conveniently and easily.

This is such a complete database that includes almost whole characters of terminators. Users can select terminator in different length, different efficiency, and different category from our database as long as they want.

In our TE database, the structure formation of terminator is displayed. As we know, a rho-independent terminator sequence consists of stem sequence, loop sequence and T tail sequence. To make the terminator structure more clear by “ A, T, C, G”, we combine stem sequence and loop sequence into stem-loop sequence so that users can imagine the secondary structure of terminator we offer compared with its loop sequence. Besides, we also provide full sequence and T tail sequence, which can help users choose terminator in other way.

The sources of terminator in our database are from the biobricks of partsregistry.org, papers we have read and database. And we selected part of whole terminators we had search which had been proved that they can work. What’s more, we offered every terminator’s efficiency.