2026-09-20T17:43:22Z https://www.ideals.illinois.edu/oai-pmh

oai:www.ideals.illinois.edu:2142/124448 2024-09-16 col_2142_5131 col_2142_10761 com_2142_5130 com_2142_10755 com_2142_234

In this project, we study a new task in computational biology, which is Fragment An- notation of the Building Plasmid. Plasmid, a small circulated DNA, is used extensively in basic and applied biology. Plasmids play a significant role in numerous computational biology experiments, emphasizing the necessity to construct them. During the making process of the plasmid, instead of synthesizing the whole plasmid, we can attempt to use the assembly method to create them. However, to apply the assembly method, we have to reuse the existing fragment to lower the cost. To this end, we formulate a new task, Fragment Annotation, which is to find the reuse 100% match fragment of the given plasmid to lower the cost when assembly the plasmid. To achieve that, We designed a greedy-based method in three different kinds of versions, which are vanilla, iteratively, and one-shot iteratively. We further examine the performance of the plasmid dataset from the PlasmidMaker paper. We evaluate the method through 2 different kinds of metrics, accuracy and cost reduction. In the cost analysis, we find a 70% drop in the cost when applying the one-shot iteratively method, which shows the effectiveness of our method. The new algorithm has been incorporated into a state-of-the-art system, called PlasmidMaker, enabling the system to reduce its cost in supporting many biosynthesis tasks. Text eng https://hdl.handle.net/2142/124448 Copyright 2024 Mu-Chun Wang Zhai, Chengxiang 2024-05 application/pdf en text Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2024-09-16 without embargo terms The student, Mu-Chun Wang, accepted the attached license on 2024-05-01 at 15:16. The student, Mu-Chun Wang, submitted this Thesis for approval on 2024-05-01 at 15:24. This Thesis was approved for publication on 2024-05-02 at 11:12. DSpace SAF Submission Ingestion Package generated from Vireo submission #20732 on 2024-09-16 at 00:37:42 Towards an intelligent system for biosynthesis: fragment annotation of the building plasmid Wang, Mu-Chun 2024-05-02 Plasmid Fragment Annotation M.S. Thesis Computer Science University of Illinois at Urbana-Champaign Computer Science