Team:Johns Hopkins-Software/theSoftware overview
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AutoGene is an all-encompassing plasmid design suite meant to streamline the process of both annotating and building sequences. Consisting of two modules -- AutoPlasmid and AutoDesign -- it first uses a highly curated database of features to search an imported plasmid, scanning the sequence for both perfect and imperfect alignments, and then generating an interactive visualization of the annotated plasmid. Once a plasmid is annotated, a user is then able to alter its contents, using the AutoGene feature database, the biobrick database, as well as custom components. The design module enables structural optimization by maintaining sets of sequence rules and taking an algorithmic approach to minimizing structural violations. Additionally the program reduces the problems caused by restriction sites during application of designs, and proposes the most suitable enzyme selections through an analysis of standard restriction sites libraries. | AutoGene is an all-encompassing plasmid design suite meant to streamline the process of both annotating and building sequences. Consisting of two modules -- AutoPlasmid and AutoDesign -- it first uses a highly curated database of features to search an imported plasmid, scanning the sequence for both perfect and imperfect alignments, and then generating an interactive visualization of the annotated plasmid. Once a plasmid is annotated, a user is then able to alter its contents, using the AutoGene feature database, the biobrick database, as well as custom components. The design module enables structural optimization by maintaining sets of sequence rules and taking an algorithmic approach to minimizing structural violations. Additionally the program reduces the problems caused by restriction sites during application of designs, and proposes the most suitable enzyme selections through an analysis of standard restriction sites libraries. | ||
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Primer design is one of the most common computational tasks in synthetic biology. In order to synthesize a DNA sequence, it is necessary to break the total sequence into small, overlapping parts, which are then combined using PCR. Once we finish this feature, Autogene will truly encompass all portions of plasmid design, using the simple philosophy of Scan/Edit/Print. From the annotation of the starting sequence, to the gathering and arranging of desired features, to the development of building blocks to actually synthesize the given sequence, everything will be done through Autogene. | Primer design is one of the most common computational tasks in synthetic biology. In order to synthesize a DNA sequence, it is necessary to break the total sequence into small, overlapping parts, which are then combined using PCR. Once we finish this feature, Autogene will truly encompass all portions of plasmid design, using the simple philosophy of Scan/Edit/Print. From the annotation of the starting sequence, to the gathering and arranging of desired features, to the development of building blocks to actually synthesize the given sequence, everything will be done through Autogene. | ||
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- | Autogene is the first tool of its kind in many ways, and we hope that its development will demonstrate the potential of many new techniques and technologies when applied to synthetic biology. By exporting our alignments to the cloud, we’ve shown that complex computation, the kind that before could only be performed on very high-powered computers, can be accessed by anyone with an internet connection. An increase in computational power for every researcher across the board could revolutionize synthetic biology, and scientific research in general. | + | Autogene is the first tool of its kind in many ways, and we hope that its development will demonstrate the potential of many new techniques and technologies when applied to synthetic biology. By exporting our alignments to the cloud, we’ve shown that complex computation, the kind that before could only be performed on very high-powered computers, can be accessed by anyone with an internet connection. An increase in computational power for every researcher across the board could revolutionize synthetic biology, and scientific research in general.</font> |
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Revision as of 05:09, 3 October 2012