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研究生:陳宏鎧
研究生(外文):Chen, Hong-Kai
論文名稱:以編碼區序列及具適應性之權重投票策略對牛津奈米孔定序進行錯誤校正
論文名稱(外文):An Adaptive Weighted Majority Vote Strategy For Polishing Nanopore-Assembled Genomes Using Coding Sequences
指導教授:黃耀廷
指導教授(外文):Huang, Yao-Ting
口試委員:高孟駿施純傑
口試委員(外文):Kao, Mong-JenShih, Chun-Chieh
口試日期:2020-01-16
學位類別:碩士
校院名稱:國立中正大學
系所名稱:資訊工程研究所
學門:工程學門
學類:電資工程學類
論文種類:學術論文
論文出版年:2020
畢業學年度:108
語文別:中文
論文頁數:34
中文關鍵詞:第三代定序基因體錯誤校正編碼區序列
外文關鍵詞:third-generation sequencinggenome polishingcoding sequences
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第三代定序技術相比於第二代定序技術,能在短時間內定序長片段,然而有較高的錯誤率,儘管透過各種基因體錯誤校正軟體修正後,仍然有約1%的錯誤無法修正。本實驗室先前的研究使用同源物種之編碼區序列(Coding sequences)進行修正剩餘的1%錯誤。雖然許多菌株有良好的修正效果,但對於缺乏編碼序列之罕見菌種,無法達到好的校正效果。因此本論文欲改良先前軟體,是針對編碼資料完整度不同之菌種,有個別客製化的修正方式。我們收集更大量的編碼序列,並藉由統計觀察罕見和常見菌種之特性,分別給予不同之校正法。實驗結果指出改良後之軟體可改善罕見與常見菌種之校正效果。
The third-generation sequencing technology generates longer reads at the cost of a higher error rate than that of next-generation sequencing technology. Even though the genome can be polished by a number of correction software, there are still about 1\% of errors remained in the genome. Previous works in our lab have demonstrated that protein-coding sequences can be used to polish the remaining 1\% errors. Although many errors were removed by this approach, the correction power is limited in the rare bacterial species lack of coding sequence in the database. Therefore, this thesis aims to improve previous methods in order to polish both common and rare bacterial species. Our method collected a larger amount of coding sequences and adaptively polished common and rare genomes according to distinct statistics and criteria. The experimental results indicated that the new software can improve correction power both in common and rare species.
論文摘要 I
Abstract II
誌謝 III
目錄 IV
圖目錄 VI
表目錄 VIII
1 介紹 1
2 文獻綜述 6
2.1 Minimap2 6
2.2 質量分數 6
3 研究方法 7
3.1 資料庫收集 8
3.2 編碼區序列預測 10
3.3 基因體修正 12
3.4 使用投票Top1%和30%編碼區序列進行修正 13
4 實驗設計與結果. 14
4.1 材料 14
4.2 實驗動機 16
4.3 實驗流程 18
4.4 實驗結果 19
4.4.1罕見菌種修正方法與結果 19
4.4.2常見菌種修正方法與結果 22
5 討論 28
5.1 Kingdom vs Genus level編碼區序列資料庫比較 29
6 結論 30
參考文獻 31

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