Ridho, Felza (2023) Analisis Immuno-Bioinformatics Pada Conserved Sequence Virus SARS-CoV-2 Yang Diperoleh Menggunakan Progressive Multiple Sequence Alignment Dan Boolean Logic. Masters thesis, Institut Teknologi Sepuluh Nopember.
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Abstract
Pada akhir tahun 2019 ditemukan virus yang hingga saat ini menjadi pandemi yaitu virus SARS-CoV-2. Akibat yang disebabkan virus ini telah dirasakan seluruh dunia. Selain virus yang muncul diawal tahun 2019 telah muncul varian-varian yang beragam, mulai dari virus yang muncul di kota Wuhan hingga varian virus omicron yang terbaru yaitu BA.5. Dengan munculnya varian virus SARS-CoV-2 dan penyebaran dari virus yang masih terus berlangsung hingga saat ini, perlu dilakukan proses untuk menemukan sequence DNA yang tidak berubah dari awal kemunculan hingga varian yang terakhir muncul yang disebut dengan conserved sequence. Dalam proses mencari conserved sequence, multiple sequence alignment dengan metode progressive dan boolean logic digunakan untuk menganalisis elemen pada sequence satu-persatu. Dari conserved sequence yang didapatkan digunakan sebagai acuan untuk analisis kandidat vaksin dengan analisis immuno-bioinformatics berbasis prediksi epitop sel B yang kemudian membentuk peptida yang dapat digunakan sebagai kandidat vaksin pada virus SARS-CoV-2. Mutasi dari sequence yang diperoleh diubah menjadi matriks jarak dengan model Kimura dan conserved sequence terpanjang diubah dalam bentuk protein translasi, kemudian dianalisis untuk menemukan peptida dari epitop sel B dan diperoleh empat peptida dengan satu di antaranya bersifat immunogen, tidak toksin dan tidak alergen sehingga dianggap sebagai kandidat vaksin.
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The SARS-CoV-2 virus, which has now become a pandemic, was discovered at the end of 2019. The consequences caused by this virus have been felt throughout the world. In addition to the virus that appeared at the beginning of 2019, various variants have appeared, starting from the virus that appeared in the city of Wuhan to the newest variant of the omicron virus, namely BA.5. With the emergence of the SARS-CoV-2 virus variant and the spread of the virus that is still ongoing today, it is necessary to carry out a process to find a DNA sequence that does not change from the first appearance to the last variant that appears, which is called a conserved sequence. In the process of searching for conserved sequences, multiple sequence alignment with the progressive method and Boolean logic are also used to analyze the elements in the sequence one by one. The conserved sequence obtained is used as a reference for vaccine candidate analysis with immuno-bioinformatics analysis based on the prediction of B cell epitopes, which then form peptides that can be used as vaccine candidates for the SARS-CoV-2 virus. The mutations from the sequences obtained were converted into a distance matrix using the Kimura model, and the longest conserved sequence was converted into a translational protein. The protein was then analyzed to find peptides from B cell epitopes, four peptides were obtained, with one of them being immunogenic, non-toxic, and non-allergenic, so it is considered a vaccine candidate.
| Item Type: | Thesis (Masters) |
|---|---|
| Uncontrolled Keywords: | SARS-CoV-2, Multiple Sequence Alignment, Metode Progressive, Conserved Sequence, Immuno-bioinformatics, Progressive method |
| Subjects: | Q Science > QA Mathematics > QA402.5 Genetic algorithms. Interior-point methods. Q Science > QA Mathematics > QA76.9 Computer algorithms. Virtual Reality. Computer simulation. Q Science > QH Biology > QH426 Genetics R Medicine > RA Public aspects of medicine > RA644.C67 COVID-19 (Disease) |
| Divisions: | Faculty of Mathematics, Computation, and Data Science > Mathematics > 44101-(S2) Master Thesis |
| Depositing User: | Felza Ridho |
| Date Deposited: | 10 Feb 2023 03:12 |
| Last Modified: | 10 Feb 2023 03:12 |
| URI: | http://repository.its.ac.id/id/eprint/96702 |
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