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A Hardware Viewpoint On Biosequence Analysis: What’s Next?

M. Graziano, S. Frache, M. Zamboni
Published 2013 · Computer Science

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Biosequence alignment recently received an increasing support from both commodity and dedicated hardware platforms. Processing capabilities are constantly rising, but still not satisfying the limitless requirements of this application. We give an insight on the contribution to this need that can possibly be expected from emerging technology devices and architectures, focusing as an example on nanofabrics based on silicon nanowires. By varying a few parameters we explore the solution space, and demonstrate with proper figures of merit how this family of beyond CMOS structures could be considered as the effective disruptive technology for biosequence analysis applications.
This paper references
10.1038/NMAT1554
Chemistry of molecules or physics of contacts?
V. Zhirnov (2006)
10.1109/NANOARCH.2011.5941486
Regular 2D NASIC-based architecture and design space exploration
C. Teodorov (2011)
Cuda compatible gpu cards as efficient hardware accelerators for smithwaterman sequence alignment. BMC Bioinf
S A Manavski (2008)
10.1002/PRO.5560040613
Comparison of methods for searching protein sequence databases
W. Pearson (1995)
Semiconductor Industry Association International technology roadmap of semiconductors, 2010 update , emerging research devices chapter
(2010)
10.1109/FCCM.2006.64
Single Pass, BLAST-Like, Approximate String Matching on FPGAs
M. Herbordt (2006)
Theoretical study of molecular quantumdot cellular automata
W. Lu (2005)
10.1088/0022-3727/39/21/R01
TOPICAL REVIEW: Semiconductor nanowires
W. Lu (2006)
10.1186/1471-2105-12-S1-S5
FPGA accelerator for protein secondary structure prediction based on the GOR algorithm
F. Xia (2011)
10.1109/ICASSP.2007.366691
High Performance Biosequence Database Scanning using FPGAs
K. Benkrid (2007)
10.1145/1084748.1084750
Nanowire-based programmable architectures
A. DeHon (2005)
10.1109/TED.2010.2052171
Effects of Parasitics and Interface Traps on Ballistic Nanowire FET in the Ultimate Quantum Capacitance Limit
K. Majumdar (2010)
10.1109/ICSICT.2008.4734599
Comparison of spintronics and nanoelectronics for information processing
K. Wang (2008)
10.1016/S0022-2836(05)80360-2
Basic local alignment search tool.
S. Altschul (1990)
Received January
(2012)
10.1109/NANO.2008.205
Image Processing Architecture for Semiconductor Nanowire Based Fabrics
P. Narayanan (2008)
10.1016/J.SSE.2012.05.022
Towards a molecular QCA wire: Simulation of write-in and read-out systems
A. Pulimeno (2012)
IEEE Trans. Electron. Devices
M Flatte (2007)
10.1109/TPDS.2009.165
A High-Performance Heterogeneous Computing Platform for Biological Sequence Analysis
Xiandong Meng (2010)
10.1109/TVLSI.2008.2005314
A Highly Parameterized and Efficient FPGA-Based Skeleton for Pairwise Biological Sequence Alignment
K. Benkrid (2009)
High-performance fully depleted silicon nanowire (diameter 5 nm) gate-all-around cmos devices
N Singh (2006)
10.1016/0022-2836(81)90087-5
Identification of common molecular subsequences.
T. Smith (1981)
Asynchronous Solutions for Nano-Magnetic Logic Circuits
M. Vacca (2015)
000-core linux supercomputer built in amazon cloud
J Brodkin (2011)
10.1023/A:1020771912723
Simulation of Field Coupled Computing Architectures Based on Magnetic Dot Arrays
György Csaba (2002)
Cuda programming guide
NVIDIA. (2011)
10.1145/2663351
Spintronics
Wang Kang (2015)
10.1186/1756-0500-4-261
DOPA: GPU-based protein alignment using database and memory access optimizations
L. Hasan (2011)
10.1109/TCAD.2009.2021008
An Outlook on Design Technologies for Future Integrated Systems
G. D. Micheli (2009)
Molecular electronics: Chemistry of molecules or physics of contacts? Nature Mater
Zhirnov (2006)
10,000-core linux supercomputer built in amazon cloud
J. Brodkin (2011)
10.1109/MDT.2011.98
Asynchrony in Quantum-Dot Cellular Automata Nanocomputation: Elixir or Poison?
M. Graziano (2011)
10.1109/NANO.2012.6322083
Silicon nanoarray circuits design, modeling, simulation and fabrication
S. Frache (2012)
10.1109/ICCD.2010.5647586
A flexible simulation methodology and tool for nanoarray-based architectures
S. Frache (2010)
10.5772/23044
An Overview of Hardware-Based Acceleration of Biological Sequence Alignment
L. Hasan (2011)
10.1201/9781439834398.ch276
Semiconductor nanowires
Wei Yang Lu (2006)
10.1109/DATE.2007.364654
Improving the Fault Tolerance of Nanometric PLA Designs
F. Angiolini (2007)
10.1109/TNANO.2012.2207965
Majority Voter Full Characterization for Nanomagnet Logic Circuits
M. Vacca (2012)
Manufacturing pathway and associated challenges for nanoscale computational systems
P. Narayanan (2009)
International technology roadmap of semiconductors, 2010 update, emerging research devices chapter
Semiconductor Industry Association. (2010)
10.1109/PDP.2010.93
Efficient Smith-Waterman on Multi-core with FastFlow
Marco Aldinucci (2010)
FETToy 2.0 source code download
Fettoy (2005)
10.1186/1471-2105-8-474
High-throughput sequence alignment using Graphics Processing Units
M. Schatz (2007)
10.1109/fccm.2007.11
FPGA-accelerated seed generation in Mercury BLASTP
Arpith C. Jacob (2007)
10.1109/TCSI.2010.2046257
Turbo NOC: A Framework for the Design of Network-on-Chip-Based Turbo Decoder Architectures
M. Martina (2010)
10.1186/1471-2105-9-S2-S10
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
Svetlin Manavski (2008)
A 160-kilobit molecular memory electronic memory patterned at 1011 bits per square centimeter
J E Green (2007)
10.1109/LED.2006.873381
High-performance fully depleted silicon nanowire (diameter /spl les/ 5 nm) gate-all-around CMOS devices
N. Singh (2006)
Activities of the Emerging Research Devices (ERD) chapter of the International Technology Roadmap for Semiconductors
C. Meyer (2004)
A Hardware Viewpoint on Biosequence Analysis
GrazianoMariagrazia (2013)
10.1145/2765491.2765520
ToPoliNano: Nanoarchitectures design made real
S. Frache (2012)
10.1186/1471-2105-12-221
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
T. Rognes (2011)
10.1021/NL035117A
Direct Observation of Nanoscale Switching Centers in Metal/Molecule/Metal Structures
C. Lau (2004)
10.1186/1471-2105-12-466
Accelerated large-scale multiple sequence alignment
Scott Lloyd (2011)
10.1088/0957-4484/4/1/004
Quantum Cellular Automata
C. Lent (1993)
10.1093/bioinformatics/btl582
Striped Smith-Waterman speeds database searches six times over other SIMD implementations
M. Farrar (2007)
10.1109/BIPOL.2007.4351855
More Than Moore's Law: Nanofabrics and Architectures
K. Wang (2007)
Quantum cellular automata. Nanotechnol
C Lent (1993)
10.1109/JSTQE.2003.812501
A biosequence processor based on free-space optical interconnect
Tao Ao (2003)
10.1007/s10825-005-7120-y
Theoretical Study of Molecular Quantum-Dot Cellular Automata
Y. Lu (2004)
10.1109/ICECS.2012.6463779
Protein alignment HW/SW optimizations
Gianvito Urgese (2012)
10.1109/FPT.2006.270389
Seed-based genomic sequence comparison using a FPGA/FLASH accelerator
D. Lavenier (2006)
10.1186/1756-0500-3-93
CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions
Yongchao Liu (2010)
10.1002/1439-7641(20020617)3:6<519::AID-CPHC519>3.0.CO;2-2
Two-dimensional molecular electronics circuits.
Y. Luo (2002)
10.1109/NANOARCH.2011.5941489
Nanofabric power analysis: Biosequence alignment case study
S. Frache (2011)
Cuda programming guide. Version 3.2
Nvidia (2011)
10.1145/1870109.1870120
ACM Journal on Emerging Technologies in Computing Systems
M. Singh (2010)
10.1145/2043643.2043645
Asynchronous Solutions for Nanomagnetic Logic Circuits
M. Vacca (2011)
10.1038/nature05462
A 160-kilobit molecular electronic memory patterned at 1011 bits per square centimetre
J. Green (2007)
10.1109/TVLSI.2011.2148183
UDSM Trends Comparison: From Technology Roadmap to UltraSparc Niagara2
A. Pulimeno (2012)



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