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Spletna aplikacija za optimizacijo rabe kodonov
ID Hekić, Uroš (Author), ID Šajn, Luka (Mentor) More about this mentor... This link opens in a new window, ID Špendl, Martin (Comentor)

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Abstract
Optimizacija rabe kodonov je postopek za zamenjavo sinonimnih kodonov z namenom prilagajanja rabe kodonov gostiteljskega organizma, ki se uporablja v predpripravi sinteze proteinov npr. pri izdelavi zdravil, dodatkov v živilski industriji ali pri preučevanju lastnosti proteinov v laboratoriju. Neoptimalno rabo kodonov spremlja nizek izkoristek izražanja, nepravilno zvijanje proteinov in s tem neuporaben končni produkt, zato je optimizacija ključen postopek pri pripravi sintetičnih proteinov. Zasnovali in implementirali smo spletno aplikacijo za interaktivno optimizacijo kodonov v realnem času na podlagi simulacije časa translacije. Načrtovali in implementirali smo več algoritmov za optimizacijo rabe kodonov in jih primerjali med sabo. Aplikacija temelji na algoritmu RTA* z globino 1, ki dosega 55% +/- 5% izboljšanje relativne napake. Aplikacija zajema celoten postopek priprave zaporedja za optimizacijo na osnovi strukture proteina. Aplikacijo smo predstavili ciljnim uporabnikom ter njihov odziv preverili z anketo. Kar 91% anketiranih uporabnikov meni, da uporabniški vmesnik podpira vse njihove zahteve pri optimizaciji kodonov. Več kot dve tretjini anketiranih meni, da je izvajanje algoritma dovolj hitro. Vsi anketirani pa bi rezultate algoritma uporabili pri svojem delu.

Language:Slovenian
Keywords:optimizacija rabe kodonov, naključni sprehod, TASEP, RTA*, spletna aplikacija, Docker, RabbitMQ
Work type:Master's thesis/paper
Typology:2.09 - Master's Thesis
Organization:FRI - Faculty of Computer and Information Science
Year:2023
PID:20.500.12556/RUL-152823 This link opens in a new window
COBISS.SI-ID:177657603 This link opens in a new window
Publication date in RUL:08.12.2023
Views:657
Downloads:97
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Secondary language

Language:English
Title:Web application for codon usage optimization
Abstract:
Codon usage optimization is a method for replacing synonymous codons in order to adapt the codon usage of the host organism. It is used in the preparation of protein synthesis, e.g. in the production of drugs, food industry additives, or in the study of protein properties in the laboratory. Suboptimal codon usage leads to a low expression efficiency, improper protein folding, and consequently, an unusable final product. Hence, optimization is a crucial step in the preparation of synthetic proteins. We have designed and implemented a web application for real-time interactive codon optimization based on translation time simulation. Multiple algorithms for codon usage optimization were designed, implemented, and compared. The application relies on the RTA* algorithm with a depth of 1, achieving a 55% +/- 5% improvement in relative error. It encompasses the entire sequence preparation process for structure-based protein optimization. We presented the application to target users and assessed their response through a questionnaire. Based on this 91% of users believe that the user interface meets all their requirements for codon optimization. More than two-thirds of respondents find the algorithm execution sufficiently fast. All respondents expressed interest in using the algorithm's results in their work.

Keywords:codon usage optimization, random walk, TASEP, RTA*, web application, Docker, RabbitMQ

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