Team:SUSTC-Shenzhen-B/future plan

Future Version of Our Software

Introduction

Now our pc software and online tool can predict the efficiency of rho-independent terminator. There are two algorithms, algorithm 1 and algorithm 2, which are based on the model created by d'Aubenton Carafa and Elena A Lesnik respectively. But when users input the sequence of their terminator, they have to choose one of the algorithms without any idea of which one is better. What’s more, if the efficiency of their terminator is not suitable for them, they have to modify the terminator themselves. Thus, we want to solve these problems in the future.

Future Plan

1. Change the coefficient of the scoring formular and find the best algorithm

D Score = nT * 18.16 + deltaG / LH * 96.59 – 116.87

(nT is the score of t tail, deltaG is the energy change of the stemloop formation and LH is the length of stemloop sequence.)

Here the coefficient of each terms can be adjusted to help make the best simulation between score and efficiency. Similarly, the calculation of E Score can also be improved.

What’s more, we want to find out which algorithm can better predict the efficiency based on our experiment data.Then users don’t need to hesitate to choose algorithm.

2. Modify the terminator sequence to match the user selected efficiency

Sometimes the user wants a terminator with specific efficiency. If the current efficiency of users terminator is not the one he want, our program can do mutation on terminator sequences and evolve a terminator that meets the requirement of efficiency.