This area is for writing your GenoCon2 Report. The guidelines below are for writing a 6 section report. An image should also be included.
Name: RIKEN GenoCon
Affiliation: RIKEN The Institute of Physical and Chemical Research
Research groups led by Professor Izui of Kinki University, Professor Sakai, and Professor Kato (currently Professor of Kyoto Gakuen University) of Kyoto University are actually trying to create such dreamlike plants. They found out that by inserting two HCHO decomposing bacterium genes into a plant (Arabidopsis thaliana), the plant got a function to remove HCHO in the air. The research teams re-design a plant pathway by adding two genes. (See details of the research)
The followings are basic explanation about key parts for Challenge B sample program.
Load the data of 5 tables (dna, promoter, protein, signal_peptide, terminator) included in the sample data (http://linkdata.org/work/rdf1s222i).
In this part, create a function to get sequences;
We named this function as ‘getSequence’. You can change the function name.
Part C. Creation a function for reverse translation
In this part, create a function to reverse translate;
We named this function as ‘reverse Translation’. You can change the function name.
Part D. Main Program
Select protein sequences registered in sample data, execute reverse translation by using the function you created in Part C, obtain DNA sequences, outputs of the execution, and display the DNA sequence in the result area.
More detail is explained in the below.
In this part, amino acids are linked to codons.
*This example is not the best. You may brash up this "map" function considering with codon optimizations to Arabidopsis and/or other idea.
*DNA sequences are represented by a letter string such as `ATGC` whereas protein sequences are represented by a letter string such as `MFLIV...`.
D-1: Obtain protein sequences
Store protein sequences in a variable named “hpsSeq”.
This function selects the "protein" table based on the variable 1, and obtain the sequence data of “Q9LBW4” in the “protein” table based on the variable 2
D-2: Reverse Translation
Translate the protein sequence stored in the variable named "hpsSeq" to a DNA sequence, by using the function created in ③, and store the DNA sequence in variable named "hpsDnaSeq".
D-3: Obtain protein sequences (in a similar way to D-1)
D-4: Reverse translation (in a similar way to D-2)
D-5: Concatenate two DNA sequences
Concatenate two DNA sequences “hpsDnaSeq” (reverse translated in ④-2) and “phiDnaSeq” (reverse translated in ④-4), and store the DNA sequence in variable named “dnaSeq”.
D-6: Display the result
Display the DNA sequence “dnaSeq” in the program executing area.
HTML tags are embedded in the result display area. By appending the strings of DNA sequence into the tag, the design results are displayed.
The plant should get the function to eliminate formaldehyde by inserting two enzymes, HPS (3-hexulose-6-phosphate synthase) and PHI (6-phospho-3-hexuloisomerase) into the Calvin Cycle of the plant.
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