Team:CBNU-Korea/Project/GD/Analysis

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					<p>2012 iGEM</p>
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				<h2>Minimal Genome Designer</h2>
				<h3>- Analysis</h3>
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					<h1>1. Overview</h1>
					<h2>1-1. Predicting Essential Genes</h2>
					<p>
						<strong>1) Need of the Analysis of Essential Genes</strong>
					</p>
					<p>It is thought that today, Synthetic Biology has reached a
						plateau. Since the success of the experiment that re-synthesizes
						the genome and insert it into the cell, it seems that Synthetic
						Biology is not developing. But if somebody can design a genome and
						synthesize it, synthetic biology can take off again. Then what do
						we need to design a genome? First, we need information about
						essential genes. An essential gene is a gene that is critical for
						survival. If you have the information about the essential gene,
						you are in a superior state in making human artificial cell in a
						true sense. Because it means that you already have the ability to
						make the brick. All you have to do is make a brick with our
						program developed for you according to the sequence of the
						essential genes, and conduct experiments.</p>
					<p>
						<strong>2) The Present of the Analysis of Essential Genes</strong>
					</p>
					<p>Essential genes are being analyzed in many places, such as
						in DEG or PATRIC.</p>
					<img src="https://static.igem.org/mediawiki/2012/1/11/CBK_B_001.png">
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						<strong>3) The Problem of the Analysis of Essential Genes</strong>
					</p>
					<p>Essential genes known today are mostly discovered with in
						vitro experiments. As seen in the chart above, the result of the
						experiment can vary according to conditions and methods. We bring
						forth a problem about this. We believe that to give meaning to a
						result, it has to be accurate. Also the analysis method of
						essential genes used today takes a lot of time and labor. To
						address this we use a bio-informatics way and find essential
						genes.</p>

					<h2>1-2. Analysis of Essential Genes</h2>
					<p>
						<strong>1) Definition of Essential Genes</strong>
					</p>
					<p>As we are using the computer to find essential genes, we
						can't use the existing method to analogize essential genes with
						experiments. We assume that if essential genes are critical to
						living, every organism must have it. So we approached the problem
						with the assumption that an essential gene is a gene that every
						living thing will has.</p>
					<p>
						<strong>2) Significance of the Analysis of Essential
							Genes</strong>
					</p>
					<p>We are proud of our analysis methods. You will see that our
						analysis result is not that different from that proved with
						experiments. Our analysis results do more than finding essential
						genes. With this, you can understand the metabolic process and
						furthermore have a good chance to synthesize an artificial cell.</p>

					<h2>1-3. Developing of the Minimal Genome Designer</h2>
					<p>
						<strong>1) The Purpose of Minimal Genome Designer</strong>
					</p>
					<p>The purpose of our program is fundamentally to understand
						the structure and the principle of the genome. However, we will
						not stop at understanding the information about genome, but hope
						that you can go on to build your own genome by using the brick in
						your experiment.</p>
					<p>
						<strong>2) Advantages of Minimal Genome Designer</strong>
					</p>
					<p>Minimal Genome Designer will make you easily understand the
						genome, by showing you the structure. Providing various
						information about the gene and the genome, our program will
						shorten your time to design the experiment. This also means that
						you can save money as well. We have tried and verified so that
						Minimal Genome Designer can procure reliability. The results made
						by Minimal Genome Designer can be used as a new background
						information for your experiment.</p>
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					<h1>2. Function</h1>

					<h2>2-1. Viewer</h2>

					<p>1) The program is installed and run in a local computer. The
						local database isn't included in the program, and to see the
						database you should have access to the server that we constructed.
					</p>
					<p>2) The program consists of the circular viewer on the upper
						left, and the linear viewer below, and a Genome list on the right.</p>
					<p>3) First, select a gene in the Genome List on the right. You
						may select it on the Tree View, or by searching the gene that you
						want. After selection, the information of the gene will be shown
						in graphic. You can see more information about the relevant gene
						and the genome on the Genome Information in the middle.</p>
					<p>4) If you move the reading glass image of the circular
						viewer, you can see the relevant location in linear graphic. By
						using the linear scroll bar, you can change the linear location.
						If you click the relevant square image in the linear viewer, you
						can see more information about the gene(Like sequences, length,
						location, Synb_id, function, product and more).</p>
					<p>5) With the check box on the lower right-hand corner of the
						circular viewer, you can check the gene of your choice.</p>
					<p>6) By checking the By COG check box, you can see each of the
						COG functions of each gene. Choose the COG function in the scroll
						box that appears after you check, then you can see the genes
						including that function.</p>
					<p>7) If you check the DEG Only check box, you can see the
						informations that DEG has found in vitro in visual.</p>
					<p>8) If you check the EG Only check box, you can see the
						information on essential genes that we gain through analysis in
						visual.</p>
					<p>9) Select 'History' in the Genome List menu, then you can
						see all the genes that have seen all along easily.</p>

					<h2>2-2. Unique Genome Designer</h2>

					<p>1) Shows the information of essential genes that can exist
						in each section.(Function, Product, COG number etc.)</p>
					<p>2) Shows the frequency of the essential genes in each
						section that are analyzed using 82 different species.</p>
					<p>3) Shows the frequency of the COG of each section that is
						analyzed using 82 different species.</p>
					<p>4) By choosing each section of 20 in the screen, the
						essential genes that can be inserted in the relevant area will be
						listed.</p>
					<p>5) The user can put the wanted essential gene In each
						section and see the processing situation. When the whole 478
						essential genes are put in all sections, the design is completed.
					</p>
					<p>7) The user can save and import the designing situation as a
						XML form at their convenience.</p>
					<p>8) When the user complete the design, the designed minimal
						genome can be saved as a XML form and it could be viewed at
						Viewer.</p>
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					<h1>3. Future Work</h1>
					<p>
						Our ultimate objective is to make a program that can build a
						complete minimum genome. Well do we know the information that we
						need to realize our goal. First, we analogize essential genes that
						every species is supposed to have. And we are aware of the fact
						that to achieve this goal, our analysis method needs higher
						reliability. Therefore, we are going to use the same method on a
						different genus (For example, like Mycoplasma, Salmonella, that
						the essential gene is already identified experimentally), and
						secure the reliability of our analysis method. Secondly, we
						presume specific genes which reflect the characteristic of genome.
						We think that there are genes that the function of it can
						represent each genome or each level. In this year we only analyzed
						every genome in Streptococcus, so we cannot provide information of
						specific genes. But we expect that the specific genes that we
						analyzed in this year not only make our software more wealthy but
						also make accurate result. Thirdly, we presume accurate
						arrangement of essential gene that we analyzed. Because we mostly
						concentrated on the analysis of strand pattern, it isn’t enough to
						provide accurate arrangement. However we know that we need the
						information of the order of genes to make complete design
						software. Thus we are going to analyze this and improve the
						completeness of our Designer.<br> We believe that if this
						analysis becomes perfect, our analysis method will secure
						reliability and give you the accurate outcome. Also hoping that
						you will use our program more actively, we are planning to provide
						information you will need(For example, restriction enzyme sites,
						Gene map, the culture conditions of different species). We hope
						our program Minimal Genome Designer will provide the fundamental
						information for your experiment in the near future.
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