Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing

作者: Michael Ruehle , Gavin Stone , Pieter Van Rooyen , Mark Hahm , Rami Mehio

DOI:

关键词:

摘要: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, genomics platform pipeline The includes one or more of first integrated circuit, where each circuit forms central processing unit (CPU) that responsive to software algorithms are configured instruct the CPU perform set genomic steps pipeline. Additionally, second also provided, forming field programmable gate array (FPGA), FPGA being by firmware arrange hardwired digital logic circuits interconnected plurality physical interconnects pipeline, arranged as engines steps. shared memory

参考文章(175)
Michael C Schatz, Ben Langmead, Steven L Salzberg, Cloud computing and the DNA data race Nature Biotechnology. ,vol. 28, pp. 691- 693 ,(2010) , 10.1038/NBT0710-691
Thomas Derrien, Jordi Estellé, Santiago Marco Sola, David G. Knowles, Emanuele Raineri, Roderic Guigó, Paolo Ribeca, Fast Computation and Applications of Genome Mappability PLoS ONE. ,vol. 7, pp. e30377- 16 ,(2012) , 10.1371/JOURNAL.PONE.0030377
Tim Oliver, Bertil Schmidt, Douglas Maskell, Hyper customized processors for bio-sequence database scanning on FPGAs Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays - FPGA '05. pp. 229- 237 ,(2005) , 10.1145/1046192.1046222
C. Burks, DNA sequence assembly IEEE Engineering in Medicine and Biology Magazine. ,vol. 13, pp. 771- 773 ,(1994) , 10.1109/51.334645
Nils Homer, Barry Merriman, Stanley F. Nelson, BFAST: An Alignment Tool for Large Scale Genome Resequencing PLoS ONE. ,vol. 4, pp. e7767- 12 ,(2009) , 10.1371/JOURNAL.PONE.0007767
Xinyu Guo, Hong Wang, Vijay Devabhaktuni, A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm International Scholarly Research Notices. ,vol. 2012, pp. 195658- 195658 ,(2012) , 10.5402/2012/195658
Nahri Moreano, Samuel Ferraz, Evaluating Optimization Strategies for HMMer Acceleration on GPU international conference on parallel and distributed systems. pp. 59- 68 ,(2013) , 10.1109/.20
Joseph Lancaster, Jeremy Buhler, Roger D. Chamberlain, Acceleration of ungapped extension in Mercury BLAST Microprocessors and Microsystems. ,vol. 33, pp. 281- 289 ,(2009) , 10.1016/J.MICPRO.2009.02.007
Yoshiki YAMAGUCHI, Tsutomu MARUYAMA, Akihiko KONAGAYA, High speed homology search with FPGAs. pacific symposium on biocomputing. pp. 271- 282 ,(2001) , 10.1142/9789812799623_0025
Khaled Benkrid, Panagiotis Velentzas, Server Kasap, A High Performance Reconfigurable Core for Motif Searching Using Profile HMM adaptive hardware and systems. pp. 285- 292 ,(2008) , 10.1109/AHS.2008.16