TY - JOUR AU - Pop, M. AU - Salzberg, S. L. PY - 2008 DA - 2008// TI - Bioinformatics challenges of new sequencing technology JO - Trends in Genetics VL - 24 UR - https://doi.org/10.1016/j.tig.2007.12.006 DO - 10.1016/j.tig.2007.12.006 ID - Pop2008 ER - TY - JOUR AU - Smith, T. F. AU - Waterman, M. S. PY - 1981 DA - 1981// TI - Identification of common molecular subsequences JO - Journal of Molecular Biology VL - 147 UR - https://doi.org/10.1016/0022-2836(81)90087-5 DO - 10.1016/0022-2836(81)90087-5 ID - Smith1981 ER - TY - JOUR AU - Rognes, T. AU - Seeberg, E. PY - 2000 DA - 2000// TI - Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors JO - Bioinformatics VL - 16 UR - https://doi.org/10.1093/bioinformatics/16.8.699 DO - 10.1093/bioinformatics/16.8.699 ID - Rognes2000 ER - TY - JOUR AU - Farrar, M. PY - 2007 DA - 2007// TI - Striped Smith-Waterman speeds database searches six times over other SIMD implementations JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl582 DO - 10.1093/bioinformatics/btl582 ID - Farrar2007 ER - TY - JOUR AU - Pearson, W. R. PY - 1991 DA - 1991// TI - Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms JO - Genomics VL - 11 UR - https://doi.org/10.1016/0888-7543(91)90071-L DO - 10.1016/0888-7543(91)90071-L ID - Pearson1991 ER - TY - CHAP AU - Liu, W. AU - Schmidt, B. AU - Voss, G. AU - Schroeder, A. AU - Muller-Wittig, W. PY - 2006 DA - 2006// TI - Bio-sequence database scanning on a GPU BT - Proceedings of the 20th IEEE International Parallel & Distributed Processing Symposium ID - Liu2006 ER - TY - CHAP AU - Sachdeva, V. AU - Kistler, M. AU - Speight, E. AU - Tzeng, T. K. PY - 2007 DA - 2007// TI - Exploring the viability of the Cell Broadband Engine for bioinformatics applications BT - Proceedings of IEEE International Parallel and Distributed Processing Symposium, CA, USA ID - Sachdeva2007 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - STD TI - Timelogic SeqCruncher™ PCIe accelerator card[http://www.timelogic.com/seqcruncher.html] UR - http://www.timelogic.com/seqcruncher.html ID - ref9 ER - TY - CHAP AU - Jacob, A. AU - Lancaster, J. AU - Buhler, J. AU - Chamberlain, R. D. PY - 2007 DA - 2007// TI - FPGA-accelerated seed generation in Mercury BLASTP BT - Proceedings of 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines UR - https://doi.org/10.1109/FCCM.2007.11 DO - 10.1109/FCCM.2007.11 ID - Jacob2007 ER - TY - JOUR AU - Lavenier, D. AU - Georges, G. AU - Liu, X. PY - 2007 DA - 2007// TI - A reconfigurable index FLASH memory tailored to seed-based genomic sequence somparison algorithms JO - VLSI Signal Processing VL - 48 UR - https://doi.org/10.1007/s11265-007-0073-6 DO - 10.1007/s11265-007-0073-6 ID - Lavenier2007 ER - TY - CHAP AU - Fei, X. AU - Yong, D. AU - Jinbo, X. PY - 2008 DA - 2008// TI - FPGA-based accelerators for BLAST families with multi-seeds detection and parallel extension BT - Proceedings of the 2nd International Conference in Bioinformatics and Biomedical Engineering ID - Fei2008 ER - TY - CHAP AU - Zhang, H. AU - Schmidt, B. AU - Mueller-Wittig, W. PY - 2008 DA - 2008// TI - Accelerating BLASTP on the Cell Broadband Engines BT - Proceedings of Pattern Recognition in Bioinformatics, Third IAPR International Conference UR - https://doi.org/10.1007/978-3-540-88436-1_39 DO - 10.1007/978-3-540-88436-1_39 ID - Zhang2008 ER - TY - JOUR AU - Roytberg, M. AU - Gambin, A. AU - Noe, L. AU - Lasota, S. AU - Furletova, E. AU - Szczurek, E. AU - Kucherov, G. PY - 2009 DA - 2009// TI - On subset seeds for protein alignment JO - IEEE/ACM Trans Comput Biol Bioinformatics VL - 6 UR - https://doi.org/10.1109/TCBB.2009.4 DO - 10.1109/TCBB.2009.4 ID - Roytberg2009 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Research VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Chao, K. M. AU - Pearson, W. R. AU - Miller, W. C. PY - 1992 DA - 1992// TI - Aligning two sequences within a specified diagonal band JO - Computer Applications in the Biosciences VL - 8 ID - Chao1992 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. PY - 1996 DA - 1996// TI - Local alignment statistics JO - Methods Enzymol VL - 266 UR - https://doi.org/10.1016/S0076-6879(96)66029-7 DO - 10.1016/S0076-6879(96)66029-7 ID - Altschul1996 ER - TY - JOUR AU - Karlin, S. AU - Altschul, S. F. PY - 1990 DA - 1990// TI - Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes JO - Proc Natl Acad Sci USA VL - 87 UR - https://doi.org/10.1073/pnas.87.6.2264 DO - 10.1073/pnas.87.6.2264 ID - Karlin1990 ER - TY - JOUR AU - Yu, Y. K. AU - Altschul, S. F. PY - 2005 DA - 2005// TI - The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti070 DO - 10.1093/bioinformatics/bti070 ID - Yu2005 ER - TY - JOUR AU - Yu, Y. K. AU - Gertz, E. M. AU - Agarwala, R. AU - Schaffer, A. A. AU - Altschul, S. F. PY - 2006 DA - 2006// TI - Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches JO - Nucleic Acids Research VL - 34 UR - https://doi.org/10.1093/nar/gkl731 DO - 10.1093/nar/gkl731 ID - Yu2006 ER - TY - STD TI - ASTRAL SCOP release 1.73[http://astral.berkeley.edu/scopseq-1.73.html] UR - http://astral.berkeley.edu/scopseq-1.73.html ID - ref21 ER - TY - STD TI - Chandonia JM, Hon G, Walker NS, Conte LL, Koehl P, Levitt M, Brenner SE: The ASTRAL compendium in 2004. Nucleic Acids Research 2004, (32 Database):D189–192. ID - ref22 ER - TY - JOUR AU - Gertz, M. AU - Yu, Y. K. AU - Agarwala, R. AU - Schaffer, A. A. AU - Altschul, S. F. PY - 2006 DA - 2006// TI - Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST JO - BMC Biology VL - 4 UR - https://doi.org/10.1186/1741-7007-4-41 DO - 10.1186/1741-7007-4-41 ID - Gertz2006 ER - TY - JOUR AU - Amdahl, G. M. PY - 1988 DA - 1988// TI - Limits of Expectation JO - International Journal of High Performance Computing Applications VL - 2 UR - https://doi.org/10.1177/109434208800200107 DO - 10.1177/109434208800200107 ID - Amdahl1988 ER - TY - CHAP AU - Firasta, N. AU - Buxton, M. AU - Jinbo, P. AU - Nasri, K. AU - Kuo, S. PY - 2008 DA - 2008// BT - Intel® AVX: new frontiers in performance improvements and energy efficiency ID - Firasta2008 ER - TY - STD TI - Larrabee microarchitecture[http://www.intel.com/technology/visual/microarch.htm] UR - http://www.intel.com/technology/visual/microarch.htm ID - ref26 ER - TY - JOUR AU - Hu, W. AU - Zhang, F. X. AU - Li, L. S. PY - 2005 DA - 2005// TI - Microarchitecture of the Godson-2 processor JO - J Comput SAstralAstralci & Techno VL - 20 UR - https://doi.org/10.1007/s11390-005-0243-6 DO - 10.1007/s11390-005-0243-6 ID - Hu2005 ER -