DESIGN AND IMPLEMENTATION OF FPGA-BASED DNA SEQUENCE

[1]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[2]  Steven J. M. Jones,et al.  Slider—maximum use of probability information for alignment of short sequence reads and SNP detection , 2008, Bioinform..

[3]  Jonathan Rose,et al.  Measuring the Gap Between FPGAs and ASICs , 2007, IEEE Trans. Comput. Aided Des. Integr. Circuits Syst..

[4]  Akihiko Konagaya,et al.  High Speed Homology Search with FPGAs , 2001, Pacific Symposium on Biocomputing.

[5]  Keith D. Underwood,et al.  RC-BLAST: towards a portable, cost-effective open source hardware implementation , 2005, IEEE International Parallel and Distributed Processing Symposium.

[6]  Bertil Schmidt,et al.  Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware , 2006, International Conference on Computational Science.

[7]  Fa Zhang,et al.  A parallel Smith-Waterman algorithm based on divide and conquer , 2002, Fifth International Conference on Algorithms and Architectures for Parallel Processing, 2002. Proceedings..

[8]  Sudhir Kumar,et al.  Molecular clocks: four decades of evolution , 2005, Nature Reviews Genetics.

[9]  Martin C. Herbordt,et al.  Single Pass, BLAST-Like, Approximate String Matching on FPGAs , 2006, 2006 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines.

[10]  Kevin Skadron,et al.  Accelerating Compute-Intensive Applications with GPUs and FPGAs , 2008, 2008 Symposium on Application Specific Processors.

[11]  D. Lipman,et al.  Rapid and sensitive protein similarity searches. , 1985, Science.

[12]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[13]  Yong Dou,et al.  Families of FPGA-Based Accelerators for BLAST Algorithm with Multi-seeds Detection and Parallel Extension , 2008, BIRD.

[14]  Cole Trapnell,et al.  How to map billions of short reads onto genomes , 2009, Nature Biotechnology.

[15]  Steven A. Guccione,et al.  Gene Matching Using JBits , 2002, FPL.

[16]  A.K. Halim,et al.  Development of DNA sequencing accelerator based on Smith Waterman algorithm with heuristic divide and conquer technique for FPGA implementation , 2008, 2008 International Conference on Computer and Communication Engineering.

[17]  Viktor K. Prasanna,et al.  Fast Regular Expression Matching Using FPGAs , 2001, The 9th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM'01).

[18]  H. T. Kung.  Why systolic architectures? , 1982, Computer.

[19]  Apostolos Dollas,et al.  A General Reconfigurable Architecture for the BLAST Algorithm , 2007, J. VLSI Signal Process..

[20]  Bertil Schmidt,et al.  Hyper customized processors for bio-sequence database scanning on FPGAs , 2005, FPGA '05.

[21]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[22]  Christof Teuscher,et al.  The BioWall: an electronic tissue for prototyping bio-inspired systems , 2002, Proceedings 2002 NASA/DoD Conference on Evolvable Hardware.

[23]  Brad L. Hutchings,et al.  Assisting network intrusion detection with reconfigurable hardware , 2002, Proceedings. 10th Annual IEEE Symposium on Field-Programmable Custom Computing Machines.

[24]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.