Team:Thessaloniki/Software

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Software






Overview


During the process of modeling our project, the team’s dry lab coded a software tool which designs and analyzes the sequences of toehold switches based on the inputs given to it (trigger, RBS, GFP, number of paired bases). The software tool utilizes Nupack, ViennaRNA (documentation in our Model's Page) and Python (version at least 3.6) to build and to characterize the behavior of the molecules. As handling the modeling in different types of computer software (Linux, Ubuntu, Windows) is quite challenging and a great spectrum of the values calculated depends on the software used for the analysis part, we decided to build the tool so that it is applicable in any case. Therefore, Nupack should be used in Linux or Ubuntu software and ViennaRNA in Windows.

For better understanding of our software package please visit first our Model page:

Model



Toehold Generator


Our software tool produces several toehold sequences based on what is described in our "Model". Specifically, each miRNA sequence leads to the creation of many different toehold switches, since for the length of the complementary_part the following applies:

for unpaired = 9 to #miRNA-paired: #compementary_part_i = paired + unpaired

where "#complementary_part" is the length of the complementary sequence, "#miRNA" is the length of the miRNA sequence, "paired" is the number of the paired bases given as input by the user and "unpaired" is the number of unpaired bases starting by number 9 and ending when the sum of paired and unpaired bases has been equalized to the length of the miRNA (Warning: in order for this software tool to be used, the length of the given miRNA has to be equal to at least 9 bases and the value selected for paired bases should follow the rule paired+unpaired<=#miRNA). So, one miRNA sequence has the effect of several lengths for the complementary_part being selected. Par example, for inputs paired = 9 and #miRNA = 20, #complementary_part will receive the values: 9+9 = 18, 9+10 = 19, 9+11 = 20.
The selection of different lengths of complementary_part enables us to design and analyze several toeholds which respond to only one miRNA molecule. The bases of complemantary_part will be totally complementary to each miRNA’s sub-sequence which has the same length as the value #complentary_part. Par example, for starting values #complementary_part = 18 and #miRNA = 20 the program will design 3 different toeholds, with the complementary_part being complementary to the bases of the miRNA responding to locations 1-18, 2-19 and 3-20 respectively.


  • Example with given inputs paired = 9, #miRNA = 20
    #complementary_part 18 19 20
    Complementary Bases Locations in miRNA 1-18
    2-19
    3-20     		1-19
    2-20     		1-20



Design and Analysis





Software Table


For more details on how to use the software tool please read the manuals: