Construction of mathematical model for high-level expression of foreign genes in pPIC9 vector and its verification

Bingli Wu, Lei Zha, Zepeng Du, Xiaomin Ying, Hua Li, Liyan Xu, Xiaofei Zheng, Enmin Li, Wuju Li

 

 

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1. Extract the 200bp from the recombinant plasmid, where the bases in 98-th, 99-th, and 100-th stand for the termination codon TAA or TAG or TGA.

2. Copy the above 200bp into click board and paste the sequence into the sequence window.

3. Click the Evaluation button, the related evaluation results will be displayed in the Evaluation window. The recombinant plasmid will meet the condition of high-level expression of foreign genes, if the P-Value is more than 0.5. Otherwise, the recombinant plasmid will not meet the condition.
4. If the evaluation results do not meet the condition of high-level expression of foreign genes, you can click the Design button to design the rational sequence based on the replacement of synonymous codons. At this time, you can only design one sequence in webserver mode. The design result will be displayed in Design window.

5. Example: you can copy the following sequence into the sequence window and test it (Select them and Ctrl-C, then Ctrl-V).

TTGTCCAGTT GATGCTTTGG GTAGATGTAC TAGAGATTCT TTCGTTAAGG GTTTGTCTTT CGCTAGATCC GGTGGTGATT GGGGTGAATG CTTTGCTTAA GCGGCCGCGA ATTAATTCGC CTTAGACATG ACTGTTCCTC AGTTCAAGTT GGGCACTTAC GAGAAGACCG GTCTTGCTAG ATTCTAATCA AGAGGATGTC

6. P-value is the ratio of the number of classifiers to predict the foreign gene to be highly expressed with expression level more than 100mg/L and total 1000 classifiers. For example, P-value with the value 0.7 indicates that there are 0.7*1000=700 classifiers to predict the foreign gene to be highly expressed. Therefore, more bigger the P-value, more possible the foreign gene highly expressed.
The default value is 0.8

7. It will show Error in the conditions listed below:
A. the sequence is not enough 200 bp;
B. the sequence contains letter(s) non A/T/C/G;
C. the sequence contains comma, semicolon, etc;
D. carriage return in the sequence;