Sequence alignment is a fundamentally memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing competencies. We propose Alignment-in-Memory (AIM), a framework for high-throughput sequence alignment using processing-in-memory, and evaluate it on UPMEM, the first publicly-available general-purpose programmable processing-in-memory system. Our evaluation shows that a real processing-in-memory system can substantially outperform server-grade multi-threaded CPU systems running at full-scale when performing sequence alignment for a wide variety of algorithms, read lengths, and edit distance thresho...
Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distrib...
The exponential growth of databases that contains biological information (such as protein and DNA da...
Abstract — Comparing genetic sequences is a well-known prob-lem in bioinformatics. Newly determined ...
Motivation Sequence alignment is a memory bound computation whose performance in modern systems is ...
Sequence alignment is a fundamentally memory bound computation whose performance in modern systems i...
Biological sequence alignment is an essential tool used in molecular biology and biomedical applicat...
Biological sequence alignment is an essential tool used in molecular biology and biomedical applicat...
Rapid evolution in sequencing technologies results in generating data on an enormous scale. A focal ...
The recent availability of new, less expensive high-throughput DNA sequencing technologies has yield...
honors thesisCollege of EngineeringElectrical & Computer EngineeringRajeev Balsubramonian,Precision ...
Genetic sequence alignment is an important tool for researchers. It lets them see the differences an...
Includes bibliographical references (pages 65-70).Reconfigurable computing technology has progressed...
Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distrib...
Reconfigurable computing technology has progressed to a stage where it is now pos-sible to achieve o...
Pattern matching forms the core of many applications and contributes to a significant fraction of th...
Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distrib...
The exponential growth of databases that contains biological information (such as protein and DNA da...
Abstract — Comparing genetic sequences is a well-known prob-lem in bioinformatics. Newly determined ...
Motivation Sequence alignment is a memory bound computation whose performance in modern systems is ...
Sequence alignment is a fundamentally memory bound computation whose performance in modern systems i...
Biological sequence alignment is an essential tool used in molecular biology and biomedical applicat...
Biological sequence alignment is an essential tool used in molecular biology and biomedical applicat...
Rapid evolution in sequencing technologies results in generating data on an enormous scale. A focal ...
The recent availability of new, less expensive high-throughput DNA sequencing technologies has yield...
honors thesisCollege of EngineeringElectrical & Computer EngineeringRajeev Balsubramonian,Precision ...
Genetic sequence alignment is an important tool for researchers. It lets them see the differences an...
Includes bibliographical references (pages 65-70).Reconfigurable computing technology has progressed...
Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distrib...
Reconfigurable computing technology has progressed to a stage where it is now pos-sible to achieve o...
Pattern matching forms the core of many applications and contributes to a significant fraction of th...
Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distrib...
The exponential growth of databases that contains biological information (such as protein and DNA da...
Abstract — Comparing genetic sequences is a well-known prob-lem in bioinformatics. Newly determined ...