Team:SHSBNU China/Software

• Acknowledgement
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• Judging
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• Model
  Modeling Software
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  Inspiration Description Design Results Hardware Demonstrate Prospect

Software

Background

“sgRNA”, is consisted of NGG (PAM) and 20 bp after that. The cytidine deaminase will recognize the fifth, sixth seventh sites of that 20 bp, and change the base. Each cytidine deaminase has different abilities to mutate different kinds of bases. (E.g. A to G; G to C) Without the sgRNA, the cytidine deaminase cannot repair certain sites. There is no faster and convenient way to fetch the sgRNA in a given nucleotide. In this case, by using JAVA, we designed a computer program that could easily help users to find sgRNA.

Design

We applied a certain cytidine deaminase, which can convert A to G for this computer program. That is, after stop codon (TAG, TGG, TGA) was mutated in the sequence, the target sequence can be repaired consequently. To activate it, according to the DNA codon, tryptophan (TGG) is the only amino acid that the stop codon can be corresponded. To sum up, base on the principle of certain cytidine deaminase and our goal, the program has the ability to detect all the NGG that the fifth, sixth and seventh base contains any G base of TGG in the last 20 bp. This figure shows the circumstance of each situation:

As for the program, detected partial sequence will be highlighted in pink, and the stop sequence will be highlighted in yellow. The results contain the whole original sequence that users provided, the highlighted part among that, and the detected partial sequence in another row with its locations in original sequence. The program can detect as many sgRNA as the original sequence has.

Results

For instance, a user provides a sequence:
ATGAAATCCGCTGAATATTTGAACACTTTTAGATTGAGAAATCTCGGCCTACCTGTCATGAACAATTTGCATG
ACATGTCTAAGGCGACTCGCATATCTGTTGAAACACTTCGGTTGTTAATCTATACAGCTGATTTTCGCTATAGG
ATCTACACTGTAGAAAAGAAAGGCCCAGAGAAGAGAATGAGAACCATTTACCAACCTTCTCGAGAACTTAA
AGCCTTACAAGGATGGGTTCTACGTAACATTTTAGATAAACTGTCGTCATCTCCTTTTTCTATTGGATTTGAAA
AGCACCAATCTATTTTGAATAATGCTACCCCGCATATTGGGGCAAACTTTATACTGAATATTGATTTGGAGGAT
TTTTTCCCAAGTTTAACTGCTAACAAAGTTTTTGGAGTGTTCCATTCTCTTGGTTATAATCGACTAATATCTTCA
GTTTTGACAAAAATATGTTGTTATAAAAATCTGCTACCACAAGGTGCTCCATCATCACCTAAATTAGCTAATCTA
ATATGTTCTAAACTTGATTATCGTATTCAGGGTTATGCAGGTAGTCGGGGCTTGATATATACGAGATATGCCGA
TGACCTCACCTTATCTGCACAGTCTATGAAAAAGGTTGTTAAAGCACGTGATTTTTTATTTTCTATAATCCCAA
GTGAAGGATTGGTTATTAACTCAAAAAAAACTTGTATTAGTGGGCCTCGTAGTCAGAGGAAAGTTACAGGTT
TAGTTATTTCACAAGAGAAAGTTGGGATAGGTAGAGAAAAATATAAAGAAATTAGAGCAAAGATACATCATA
TATTTTGCGGTAAGTCTTCTGAGATAGAACACGTTAGGGGATGGTTGTCATTTATTTTAAGTGTGGATTCAAA
AAGCCATAGGAGATTAATAACTTATATTAGCAAATTAGAAAAAAAATATGGAAAGAACCCTTTAAATAAAGCG
AAGACCTAA
Then, the result will be:

Where pink areas and the yellow stop codons between them are two different sgRNA, and 668bp and 844bp are the location of that.

Here is the useful applet of our project.
https://github.com/igemsoftware2019/Biotool Click here to download our applet