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Team:CBNU-Korea/Project description
From 2011.igem.org
The synthetic minimal chromosome can be a base of synthetic minimal genome which is blueprint of new organism. Also, the synthetic minimal chromosome is a unit, organized gene set of specific biological function, constructed to have minimal function by ‘ Divide and Conquer‘ strategy. Design the synthetic minimal chromosome with essential genes, we have to select specific function of essential genes and appropriately re-arrange essential genes because transcription rate can be affected by arrangement, direction of genes. For these reasons, we need to use a new analyze method with those existing information for design. We got the information what we need from DEG, NCBI and DoriC databases in order to get information about essential genes in each species, gbk files for each species and location of replication origin in each species. Then, we saved them in our database with MySQL sever. In this step, we also calculated distance between origin and each essential gene, named DTO, Distance To Origin, the shortest distance from location of origin to each essential gene. Because of difference of genome size in species, we divided genome to half of its size and each half side of genome is re-divided by 10 percent of its size. Then, we used SAS program to analyze a distribution of essential genes in each 10 percent of half side of each species. All of this work is saved in our database. We expect that it is useful genome design software when database is connected.
