Towards an intelligent system for biosynthesis: fragment annotation of the building plasmid

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.

Name thesis:degree_name

M.S.

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Computer Science

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2024

Author dc:creator

• Wang, Mu-Chun

Contributors dc:contributor

• Zhai, Chengxiang

• Plasmid
• Fragment Annotation

Statement dc:rights

• Copyright 2024 Mu-Chun Wang

Language dc:language

eng, en

Handle dc:identifier

https://hdl.handle.net/2142/124448

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/124448