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

DGIST Authors

Jeongmin Bae ; Daehoon Kim ; Min-soo Kim

Advisor

김대훈

Co-Advisor(s)

Min-soo Kim

Issued Date

2021

Awarded Date

2021/02

Citation

Jeongmin Bae. (2021). GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments. doi: 10.22677/thesis.200000362726

Type

Thesis

Subject

Primer design, GPU computation, Sequence analysis, 프라이머 디자인, GPU 연산, 시퀀스 분석

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

DOI

10.22677/thesis.200000362726

Degree

Master

Department

Information and Communication Engineering

Publisher

DGIST

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