GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments
- Title
- GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments
- Alternative Title
- 프라이머 제한 조건과 특이성 조건을 동시에 만족하는 유효한 모든 프라이머를 GPU를 활용해 빠르게 디자인하는 방법
- Author(s)
- Jeongmin Bae
- DGIST Authors
- Jeongmin Bae ; Daehoon Kim ; Min-soo Kim
- Advisor
- 김대훈
- Co-Advisor(s)
- Min-soo Kim
- Issued Date
- 2021
- Awarded Date
- 2021/02
- Type
- Thesis
- Table Of Contents
-
Ⅰ. INTRODUCTION 1
1.1 Background 1
1.2 Review of MRPrimer 3
Ⅱ. IMPLEMENTATION 6
2.1 Overview of GPrimer 6
2.2 Steps 1~3: Building Hash Maps and Processing using CPU threads 6
2.3 Step 4: Building Arrays and General Cross-Hybridization Filtering 8
2.4 Step 5: Pair Filtering and Ranking 16
Ⅲ. RESULTS 20
3.1 Experimental setup and Data sets 20
3.2 Performance Comparison with MRPrimer 21
3.3 Performance of GPrimer varying the number of GPUs 22
3.4 Effectiveness of workload balancing and streaming-copy 24
3.5 Memory usage 26
Ⅳ. CONCLUSIONS 27
Ⅴ. REFERENCES 28
- URI
-
http://dgist.dcollection.net/common/orgView/200000362726
http://hdl.handle.net/20.500.11750/16667
- Degree
- Master
- Department
- Information and Communication Engineering
- Publisher
- DGIST
- Related Researcher
-
-
Kim, Daehoon
- Research Interests Computer Architecture and Systems; Virtualization; Cloud Computing
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- Files in This Item:
-
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- Appears in Collections:
- Department of Electrical Engineering and Computer Science Theses Master
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