Team:ZJU-China/Next Generation


Bach 2011

    The next generation of our software, Bach 2011, will continue its endeavor in the freedom and mystery of gene sequence composition, but with more proficiency, versatility and craziness. Bach 2011 will hopefully supersede Bach 2010 in the following aspects:

    1. The estimation of RiPS in Bach 2010 is limited in the choice of host organism, since the parameters required by the model for RiPS output are organism specific and only those in Escherichia coli are detected and known at the moment. Bach 2011 intends to enlarge the choice to include organisms commonly adopted as chassis for biobricks, such as Saccharomyces cerevisiae. Published research results have to be looked through in order to gather more data. In the worst case, new experiments will also have to be made for the determination of such values.

    2. While Bach 2010 can interpret the input sequence in terms of RiPS to denote its translation behavior, Bach 2011 hopes to reverse the interpretation other way around. To fully utilize the insight in translation behavior based on our mathematical model, Bach 2011 will realize one of the original goals of the whole Bach program: quantitative alteration of gene sequence, which is to alter coding sequences according to the desired RiPS value. A simpler approach would be to proved users with certain levels of RiPS (such as to assign levels from fastest to slowest with numbers from 1-5 to denote its state), so that ordinary users can obtain the rewritten sequence without knowledge in the true value of RiPS. But for more advanced users who have a special need for the sequence translational behavior, Bach 2011 will keep substituting codons and rewriting sequences until finally produce the new sequence that has the same value of RiPS as the user intended.

    3. The scope of sequence alteration will also be broadened in Bach 2011. Besides coding sequences of biobricks, certain parts of non-coding sequences (such as RBS, promoter etc.) will also be considered and incorporated into the new generation. RBS especially would be our focus, for the short sequence of RBS determines the strength of ribosome attachment and greatly influence the translation initiation rate (the parameter of walpha in our model). Thus the initiation process will be drawn into detail and the sequence of RBS can be recomposed for the initiation rate and also the RiPS of desire.

    4. More factors, playing roles in the elongation process, would also to be taken into consideration in Bach 2011, including mRNA secondary structures. As many factors in the life process are hard to be quantified, such intended improvements will remain as one of the greatest challenges for our new generation of Bach.