Team:CBNU-Korea/Data

From 2011.igem.org

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Revision as of 20:03, 5 October 2011

: Our software can help user design artificial genome with essential genes in silico. However, there are no essential gene data in The Registry of Standard Biological Parts database. So, we employ way of our software using method that user design the genome with essential genes in first step, and user should modify the chosen essential genes for using biobrick assembly method in second step. Then user uses biobrick assembly methods for synthesizing the genome in wetlab. And we will submit our software to the Registry of Software tools on the web, https://github.com/igemsoftware, until Asia Regional Jamboree. Also, because of the Wiki freeze on Oct 5, we’ll introduce another web address which can download our software. Our software, GOD, is used to design artificial genome with essential genes that are stored in our database at present. We plan to analogize more essential gene data which fit on our statistical analysis and add to our database. It will make that user can design various, characterized artificial genome. Also, for easy designing in drylab and synthesizing in wetlab, we will employ data of The Registry of Standard Biological Parts database in next version of our software.

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+: Our software can help user design artificial genome with essential genes in silico. However, there are no essential gene data in The Registry of Standard Biological Parts database.
-The synthetic minimal chromosome can be a basis of the synthetic minimal genome which is blueprint of new organism. Also, the synthetic minimal chromosome is a unit, organized by a gene set of specific biological function, constructed to have minimal function described by ‘Divide and Conquer‘ strategy. To design the synthetic minimal chromosome with essential genes, we have to select the specific function of essential genes and appropriately re-arrange essential genes because the transcription rate can be affected by the arrangement and direction of genes. For these reasons, we need to use a new analyzing method with those existing information for the design.<br>
+So, we employ way of our software using method that user design the genome with essential genes in first step, and user should modify the chosen essential genes for using biobrick assembly method in second step. Then user uses biobrick assembly methods for synthesizing the genome in wetlab.
-We will use DEG, NCBI and DoriC databases in order to get information on essential genes in each species, gbk files for each species and location of replication origin in each species. Then, we will save them in our database with the MySQL sever. In this step, we will calculate the distance between the origin and each essential gene, named DTO (distance to origin), and the shortest distance from the location of origin to each essential gene. Because of the differences in genome sizes of species, we will divide the genome to half its size and each half part of the genome will be re-divided to 10 percent of its size. Then, we will use the SAS program to analyze the distribution of essential genes in each of the 10 percent portions of the half part of each species. All of this work will be saved in our database. We expect that it is a useful genome design software when the database is connected.
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+ And we will submit our software to the Registry of Software tools on the web, https://github.com/igemsoftware, until Asia Regional Jamboree. Also, because of the Wiki freeze on Oct 5, we’ll introduce another web address which can download our software.
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+Our software, GOD, is used to design artificial genome with essential genes that are stored in our database at present. We plan to analogize more essential gene data which fit on our statistical analysis and add to our database. It will make that user can design various, characterized artificial genome. Also, for easy designing in drylab and synthesizing in wetlab, we will employ data of The Registry of Standard Biological Parts database in next version of our software.
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