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Team:BostonU/Clotho
From 2013.igem.org
Clotho and Eugene
Clotho Introduction
Our project is focused on creating a standardized method for the characterization of genetic circuits in synthetic biology. In order to achieve this goal, it is necessary to have a platform that enables us to create the standardized data, organize it, and manage it efficiently. We have been utilizing Clotho, a synthetic biology software suite developed with tools for analyzing and organizing data.
This section aims to describe how we have been using Clotho in our project. We divided the content into the Clotho Apps we used, giving a brief explanation of how each app works and examples of situations in which they were useful for our project.
Blasto
Blasto can be used to verify DNA sequences by comparing a sequence with the expected sequence. Blasto shows the percentage of the match and the number of gaps between sequences and where those gaps occur. Users can create a collection of their parts and save sequences for easy comparison.
Eugene
The BosotnU iGEM team used Eugene to determine the number of permutations for transcriptional units that can be assembled from the MoClo parts and devices specified by the user. To eliminate extraneous permutations, the user must specify rules pertaining to the order and relationship between parts.
Eugene can be utilized via Clotho's Eugene Scriptor app. The
We were fortunate to be able to use Eugene through Clotho's Eugene Scriptor. The first task in writing a Eugene script is to define what the parts are. Notice that the language is very straightforward and intuitive.
In the example above, we are defining our basic parts. Although the fusion/MoClo sites themselves are not basic parts, we consider them as a separate entities because they are essential when combining different MoClo parts. At this point, fusion sites as a separate part would be a more versatile method of using the language.
After defining which parts Eugene will be combining together, the next step would be to identify the device. In this case, different basic parts are combined to form a MoClo Level 0 part.
After defining our MoClo level 0 devices, the next step is to define MoClo Level 1 devices. In this case, a Level 1 device is designated to include a promotor, RBS, gene, and terminator. Additional rules are added as needed. For instance, we are creating rules to make sure the MoClo sites of subsequent parts are the same so they are able to be ligated together. In the picture below, the rule is expressed for promoter and RBS. Additionally, we have to be consistent with the design of the MoClo parts, which means that the part can not be flanked by the same MoClo sites as shown in the second rule.
PigeonCAD
