Biobrick & Unique minimal Genome Software 2012 iGEM TEAM OF CHUNGBUK NATIONAL UNIVERSITY

CBNU-KOREA

BIOBRICK DESIGNER

MINIMAL GENOME DESIGNER

REFERENCE

Fig 7. We analyzed essential genes and the arrangement of them by our method of this. Result of this analysis are provided in the Minimal Genome Designer as a base information.

1. Yan Lin1 & Randy Ren Zhang2, 2011, Putative essential and core-essential genes in Mycoplasma genomes, Wayne State University, Detroit 48201, USA. 2. Puechberty J, Blaineau C, Meghamla S, Crobu L, Pagès M, Bastien P., 2007, Compared genomics of the strand switch region of Leishmania chromosome 1 reveal a novel genus-specific gene and

conserved structural features and sequence motifs., CNRS/Université Montpellier France. 3. Xiao Liu,*Shi-Yuan Wang and Jia Wang, 2011, A statistical feature of Hurst exponents of essential genes in bacterial genomes, Chongqing University, 174 ShaPingBa District, Chongqing, 400044, China. 4. Mario Juhas1, Leo Eberl1 and John l. Glass2, 2011, Essence of life: essential genes of minimal genomes, The J. Craig Venter Institute, Rockville, MD 20850, USA 5. Sophie Abby and vincent Daubin, 2007, Comparative genomics and the evolution of prokaryotes, Laboratoire de Biométrie et Biologie évolutive, Villeurbanne, F-69622 cedex, France 6. Doszpoly A, Benko M, Bovo G, Lapatra SE, Harrach B, 2011, Comparative analysis of a cinserved gene block from the genome of the memers of the genus ictalurivius, Hungarian Academy, Budapest.

Overview The purpose of our project is to increase the efficiency of the experiment by using the designing process of BioBrick prior to the experiment, and improve the efficiency of the connection between the next experiment conducted by the program user. Our Design The user can arrange the BioBrick in any sequence they want. And if they want, the user can put a proper Prefix, Suffix restriction enzyme site between the Bricks by the software. By selecting the Plasmid Backbone and the restriction enzyme in sequence, the cloning will be done automatically.

INTRODUCTION FEATURE FUTURE WORK

1. Commnunication

BBa_K01023

We are planning to add a communication function between the users. This function will help the users to share opinions, and discuss designing information about a specific Brick. This discussion will help the users improve their experiment or project.

FLOW CHART

Fig 2. The registered BioBrick information needed for designing in this program, can be easily downloaded without being typed in.

Fig 3. The project in designing in progress can be saved or imported. Also, by saving the informations as a SBOL, GeneBank, FASTA form, the user can use the information that they design in other programs as well.

3. Screen shot

GenBank SBOL FASTA

1. BioBrick Data Download

2. Various storage formats

Fig 4. The BioBrick that the user designed from the program is saved in image files to be readily used in Wiki or documents.

Fig 1. The user can arrange the BioBrick in any sequence they want and put a proper Prefix, Suffix restriction enzyme site between the Bricks by the software. By selecting the Plasmid Backbone and the restriction enzyme in sequence, the cloning will be done automatically.

2. View of Expression rate

Fig 5. The expression rate will be produced in a numerical value. The expression rate value is a score that will show the users how the expression of the BioBrick designed by cloning is working in the experiment. To make it as a score, theoretical background and algorithm based on a lot of data are required.

3. Registry parts of our software

UnComfortable

Comfortable

Fig 6. Simplification of the registration process of the iGEM Part will be offered. The registration of BioBrick is now available only in online. But by co-working with iGEM, we will develop a better functioning program, and make it possible to design and register the Brick at the same time. This software will find a way to deliver your desires without a bit of additional effort on your part.You more quickly, you'll get notarized.

INTRODUCTION

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.

FLOW CHART

SOFTWARE ANALYSIS RESULT

1. Searching Essential genes in Streptococcus

Fig 8. We grouped the genes with the similar sequence using the BLAST result and annotate with our own ID. If all the 82 total genome have a specific SynB UID, then we infer them as an 'Essential Gene'. The total essential genes in 82 species of Streptococcus are about 478.

2. Finding out Region of Essential genes

Fig 9. The X axis shows the 20 sections of the genome size. And the Y axis is the frequency of the genome. We can divide between the SynB UID which is the origin of high frequency and SynB UID which is the origin of high frequency by both sides.

3. Analyzing Distributions of Function of Essential genes

Fig 10. The X axis shows the 20 sections of the genome size. And the Y axis is the frequency of the gene provided the COG. The graph provide an information that the COG is distributed symmetrically around the middle of origin.

4. Estimated The Trans Regression Model

Fig 11. The X axis shows the 100 sections of the genome of the randomly selected 77 species. And the Y axis is the ratio of the + patterns of each section. when the standard number is 50, the + patterns appears as 25 on the left, and the – pattern on the right higher than 80. So in this case, it is a + pattern.

1. Viewer

Fig 12. Shows the information of genome as a circular and linear form. Users can also see the information of genes like sequence, function, product, strand and location.

Fig 13. Shows Essential genes that are provided from DEG ; Red Circle Shows Essential genes that are presumed by CBNU-Korea ; Blue Circle.

2. Designer

Fig 14. Users can design minimal genome by inserting particular essential gene into the number of the twenty particular sections of genome.

Fig 15. Users can see information of genes that are located in each section of genome. Also it is able to insert, delete or exchange a gene with other gene. These information can be seen in Viewer.