Smith–Waterman algorithm (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Smith–Waterman algorithm" in English language version.

refsWebsite

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19doi.org

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18nih.gov

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4psu.edu

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3semanticscholar.org

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3harvard.edu

18^th place

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3web.archive.org

1^st place

2nvidia.com

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1usc.edu

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1ieee.org

652^nd place

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1arxiv.org

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1ornl.gov

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1progeniq.com

low place

1tudelft.nl

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1archive.org

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1genomequest.com

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1bioinformaticsARRAYxfordjournalsARRAYrg

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1archive.today

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1googlepages.com

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archive.org

Liu, Yang; Huang, Wayne; Johnson, John; Vaidya, Sheila (2006). "GPU Accelerated Smith-Waterman". Computational Science – ICCS 2006. Lecture Notes in Computer Science. Vol. 3994. Springer. pp. 188–195. doi:10.1007/11758549_29. ISBN 978-3-540-34385-1.

archive.today

Farrar, Michael S. (2008). "Optimizing Smith–Waterman for the Cell Broadband Engine". Archived from the original on 2012-02-12. {{cite journal}}: Cite journal requires |journal= (help)

arxiv.org

Zhao, Mengyao; Lee, Wan-Ping; Garrison, Erik P; Marth, Gabor T (4 December 2013). "SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications". PLOS ONE. 8 (12): e82138. arXiv:1208.6350. Bibcode:2013PLoSO...882138Z. doi:10.1371/journal.pone.0082138. PMC 3852983. PMID 24324759.

bioinformaticsARRAYxfordjournalsARRAYrg

Rognes, Torbjørn; Seeberg, Erling (2000). "Six-fold speed-up of Smith–Waterman sequence database searches using parallel processing on common microprocessors". Bioinformatics. 16 (8): 699–706. doi:10.1093/bioinformatics/16.8.699. PMID 11099256. {{cite journal}}: External link in |journal= (help)

doi.org

Smith, Temple F. & Waterman, Michael S. (1981). "Identification of Common Molecular Subsequences" (PDF). Journal of Molecular Biology. 147 (1): 195–197. CiteSeerX 10.1.1.63.2897. doi:10.1016/0022-2836(81)90087-5. PMID 7265238.
Osamu Gotoh (1982). "An improved algorithm for matching biological sequences". Journal of Molecular Biology. 162 (3): 705–708. CiteSeerX 10.1.1.204.203. doi:10.1016/0022-2836(82)90398-9. PMID 7166760.
Stephen F. Altschul & Bruce W. Erickson (1986). "Optimal sequence alignment using affine gap costs". Bulletin of Mathematical Biology. 48 (5–6): 603–616. doi:10.1007/BF02462326. PMID 3580642. S2CID 189889143.
Miller, Webb; Myers, Eugene (1988). "Optimal alignments in linear space". Bioinformatics. 4 (1): 11–17. CiteSeerX 10.1.1.107.6989. doi:10.1093/bioinformatics/4.1.11. PMID 3382986.
Saul B. Needleman; Christian D. Wunsch (1970). "A general method applicable to the search for similarities in the amino acid sequence of two proteins". Journal of Molecular Biology. 48 (3): 443–453. doi:10.1016/0022-2836(70)90057-4. PMID 5420325.
Sankoff D. (1972). "Matching Sequences under Deletion/Insertion Constraints". Proceedings of the National Academy of Sciences of the United States of America. 69 (1): 4–6. Bibcode:1972PNAS...69....4S. doi:10.1073/pnas.69.1.4. PMC 427531. PMID 4500555.
Thomas A. Reichert; Donald N. Cohen; Andrew K.C. Wong (1973). "An application of information theory to genetic mutations and the matching of polypeptide sequences". Journal of Theoretical Biology. 42 (2): 245–261. Bibcode:1973JThBi..42..245R. doi:10.1016/0022-5193(73)90088-X. PMID 4762954.
William A. Beyer, Myron L. Stein, Temple F. Smith, and Stanislaw M. Ulam (1974). "A molecular sequence metric and evolutionary trees". Mathematical Biosciences. 19 (1–2): 9–25. doi:10.1016/0025-5564(74)90028-5.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Peter H. Sellers (1974). "On the Theory and Computation of Evolutionary Distances". SIAM Journal on Applied Mathematics. 26 (4): 787–793. doi:10.1137/0126070.
M.S Waterman; T.F Smith; W.A Beyer (1976). "Some biological sequence metrics". Advances in Mathematics. 20 (3): 367–387. doi:10.1016/0001-8708(76)90202-4.
Chowdhury, Rezaul; Le, Hai-Son; Ramachandran, Vijaya (July 2010). "Cache-oblivious dynamic programming for bioinformatics". IEEE/ACM Transactions on Computational Biology and Bioinformatics. 7 (3): 495–510. doi:10.1109/TCBB.2008.94. PMID 20671320. S2CID 2532039.
D. S. Hirschberg (1975). "A linear space algorithm for computing maximal common subsequences". Communications of the ACM. 18 (6): 341–343. CiteSeerX 10.1.1.348.4774. doi:10.1145/360825.360861. S2CID 207694727.
Wozniak, Andrzej (1997). "Using video-oriented instructions to speed up sequence comparison". Computer Applications in the Biosciences. 13 (2): 145–50. doi:10.1093/bioinformatics/13.2.145. PMID 9146961.
Farrar, Michael S. (2007). "Striped Smith–Waterman speeds database searches six times over other SIMD implementations". Bioinformatics. 23 (2): 156–161. doi:10.1093/bioinformatics/btl582. PMID 17110365.
Zhao, Mengyao; Lee, Wan-Ping; Garrison, Erik P; Marth, Gabor T (4 December 2013). "SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications". PLOS ONE. 8 (12): e82138. arXiv:1208.6350. Bibcode:2013PLoSO...882138Z. doi:10.1371/journal.pone.0082138. PMC 3852983. PMID 24324759.
Liu, Yang; Huang, Wayne; Johnson, John; Vaidya, Sheila (2006). "GPU Accelerated Smith-Waterman". Computational Science – ICCS 2006. Lecture Notes in Computer Science. Vol. 3994. Springer. pp. 188–195. doi:10.1007/11758549_29. ISBN 978-3-540-34385-1.
Manavski, Svetlin A. & Valle, Giorgio (2008). "CUDA compatible GPU cards as efficient hardware accelerators for Smith–Waterman sequence alignment". BMC Bioinformatics. 9 (Suppl 2:S10): S10. doi:10.1186/1471-2105-9-S2-S10. PMC 2323659. PMID 18387198.
Rognes, Torbjørn; Seeberg, Erling (2000). "Six-fold speed-up of Smith–Waterman sequence database searches using parallel processing on common microprocessors". Bioinformatics. 16 (8): 699–706. doi:10.1093/bioinformatics/16.8.699. PMID 11099256. {{cite journal}}: External link in |journal= (help)
Rognes, Torbjørn (2011). "Faster Smith–Waterman database searches with inter-sequence SIMD parallelisation". BMC Bioinformatics. 12: 221. doi:10.1186/1471-2105-12-221. PMC 3120707. PMID 21631914.

genomequest.com

"Bioinformatics High Throughput Sequence Search and Analysis (white paper)". GenomeQuest. Archived from the original on May 13, 2008. Retrieved 2008-05-09.

googlepages.com

farrar.michael.googlepages.com

Farrar, Michael S. (2008). "Optimizing Smith–Waterman for the Cell Broadband Engine". Archived from the original on 2012-02-12. {{cite journal}}: Cite journal requires |journal= (help)

harvard.edu

ui.adsabs.harvard.edu

Sankoff D. (1972). "Matching Sequences under Deletion/Insertion Constraints". Proceedings of the National Academy of Sciences of the United States of America. 69 (1): 4–6. Bibcode:1972PNAS...69....4S. doi:10.1073/pnas.69.1.4. PMC 427531. PMID 4500555.
Thomas A. Reichert; Donald N. Cohen; Andrew K.C. Wong (1973). "An application of information theory to genetic mutations and the matching of polypeptide sequences". Journal of Theoretical Biology. 42 (2): 245–261. Bibcode:1973JThBi..42..245R. doi:10.1016/0022-5193(73)90088-X. PMID 4762954.
Zhao, Mengyao; Lee, Wan-Ping; Garrison, Erik P; Marth, Gabor T (4 December 2013). "SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications". PLOS ONE. 8 (12): e82138. arXiv:1208.6350. Bibcode:2013PLoSO...882138Z. doi:10.1371/journal.pone.0082138. PMC 3852983. PMID 24324759.

ieee.org

ieeexplore.ieee.org

Chowdhury, Rezaul; Le, Hai-Son; Ramachandran, Vijaya (July 2010). "Cache-oblivious dynamic programming for bioinformatics". IEEE/ACM Transactions on Computational Biology and Bioinformatics. 7 (3): 495–510. doi:10.1109/TCBB.2008.94. PMID 20671320. S2CID 2532039.

nih.gov

pubmed.ncbi.nlm.nih.gov

Smith, Temple F. & Waterman, Michael S. (1981). "Identification of Common Molecular Subsequences" (PDF). Journal of Molecular Biology. 147 (1): 195–197. CiteSeerX 10.1.1.63.2897. doi:10.1016/0022-2836(81)90087-5. PMID 7265238.
Osamu Gotoh (1982). "An improved algorithm for matching biological sequences". Journal of Molecular Biology. 162 (3): 705–708. CiteSeerX 10.1.1.204.203. doi:10.1016/0022-2836(82)90398-9. PMID 7166760.
Stephen F. Altschul & Bruce W. Erickson (1986). "Optimal sequence alignment using affine gap costs". Bulletin of Mathematical Biology. 48 (5–6): 603–616. doi:10.1007/BF02462326. PMID 3580642. S2CID 189889143.
Miller, Webb; Myers, Eugene (1988). "Optimal alignments in linear space". Bioinformatics. 4 (1): 11–17. CiteSeerX 10.1.1.107.6989. doi:10.1093/bioinformatics/4.1.11. PMID 3382986.
Saul B. Needleman; Christian D. Wunsch (1970). "A general method applicable to the search for similarities in the amino acid sequence of two proteins". Journal of Molecular Biology. 48 (3): 443–453. doi:10.1016/0022-2836(70)90057-4. PMID 5420325.
Sankoff D. (1972). "Matching Sequences under Deletion/Insertion Constraints". Proceedings of the National Academy of Sciences of the United States of America. 69 (1): 4–6. Bibcode:1972PNAS...69....4S. doi:10.1073/pnas.69.1.4. PMC 427531. PMID 4500555.
Thomas A. Reichert; Donald N. Cohen; Andrew K.C. Wong (1973). "An application of information theory to genetic mutations and the matching of polypeptide sequences". Journal of Theoretical Biology. 42 (2): 245–261. Bibcode:1973JThBi..42..245R. doi:10.1016/0022-5193(73)90088-X. PMID 4762954.
Chowdhury, Rezaul; Le, Hai-Son; Ramachandran, Vijaya (July 2010). "Cache-oblivious dynamic programming for bioinformatics". IEEE/ACM Transactions on Computational Biology and Bioinformatics. 7 (3): 495–510. doi:10.1109/TCBB.2008.94. PMID 20671320. S2CID 2532039.
Wozniak, Andrzej (1997). "Using video-oriented instructions to speed up sequence comparison". Computer Applications in the Biosciences. 13 (2): 145–50. doi:10.1093/bioinformatics/13.2.145. PMID 9146961.
Farrar, Michael S. (2007). "Striped Smith–Waterman speeds database searches six times over other SIMD implementations". Bioinformatics. 23 (2): 156–161. doi:10.1093/bioinformatics/btl582. PMID 17110365.
Zhao, Mengyao; Lee, Wan-Ping; Garrison, Erik P; Marth, Gabor T (4 December 2013). "SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications". PLOS ONE. 8 (12): e82138. arXiv:1208.6350. Bibcode:2013PLoSO...882138Z. doi:10.1371/journal.pone.0082138. PMC 3852983. PMID 24324759.
Manavski, Svetlin A. & Valle, Giorgio (2008). "CUDA compatible GPU cards as efficient hardware accelerators for Smith–Waterman sequence alignment". BMC Bioinformatics. 9 (Suppl 2:S10): S10. doi:10.1186/1471-2105-9-S2-S10. PMC 2323659. PMID 18387198.
Rognes, Torbjørn; Seeberg, Erling (2000). "Six-fold speed-up of Smith–Waterman sequence database searches using parallel processing on common microprocessors". Bioinformatics. 16 (8): 699–706. doi:10.1093/bioinformatics/16.8.699. PMID 11099256. {{cite journal}}: External link in |journal= (help)
Rognes, Torbjørn (2011). "Faster Smith–Waterman database searches with inter-sequence SIMD parallelisation". BMC Bioinformatics. 12: 221. doi:10.1186/1471-2105-12-221. PMC 3120707. PMID 21631914.

ncbi.nlm.nih.gov

Sankoff D. (1972). "Matching Sequences under Deletion/Insertion Constraints". Proceedings of the National Academy of Sciences of the United States of America. 69 (1): 4–6. Bibcode:1972PNAS...69....4S. doi:10.1073/pnas.69.1.4. PMC 427531. PMID 4500555.
Zhao, Mengyao; Lee, Wan-Ping; Garrison, Erik P; Marth, Gabor T (4 December 2013). "SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications". PLOS ONE. 8 (12): e82138. arXiv:1208.6350. Bibcode:2013PLoSO...882138Z. doi:10.1371/journal.pone.0082138. PMC 3852983. PMID 24324759.
Manavski, Svetlin A. & Valle, Giorgio (2008). "CUDA compatible GPU cards as efficient hardware accelerators for Smith–Waterman sequence alignment". BMC Bioinformatics. 9 (Suppl 2:S10): S10. doi:10.1186/1471-2105-9-S2-S10. PMC 2323659. PMID 18387198.
Rognes, Torbjørn (2011). "Faster Smith–Waterman database searches with inter-sequence SIMD parallelisation". BMC Bioinformatics. 12: 221. doi:10.1186/1471-2105-12-221. PMC 3120707. PMID 21631914.

nvidia.com

"CUDA Zone". Nvidia. Retrieved 2010-02-25.
"NVIDIA Parabricks". NVIDIA. Retrieved 2024-07-11.

ornl.gov

ft.ornl.gov

FPGA 100x Papers: "Archived copy" (PDF). Archived from the original (PDF) on 2008-07-05. Retrieved 2007-10-17.{{cite web}}: CS1 maint: archived copy as title (link), "Archived copy" (PDF). Archived from the original (PDF) on 2008-07-05. Retrieved 2007-10-17.{{cite web}}: CS1 maint: archived copy as title (link), and "Archived copy" (PDF). Archived from the original (PDF) on 2011-07-20. Retrieved 2007-10-17.{{cite web}}: CS1 maint: archived copy as title (link)

progeniq.com

Progeniq Pte. Ltd., "White Paper - Accelerating Intensive Applications at 10×–50× Speedup to Remove Bottlenecks in Computational Workflows".

psu.edu

citeseerx.ist.psu.edu

Smith, Temple F. & Waterman, Michael S. (1981). "Identification of Common Molecular Subsequences" (PDF). Journal of Molecular Biology. 147 (1): 195–197. CiteSeerX 10.1.1.63.2897. doi:10.1016/0022-2836(81)90087-5. PMID 7265238.
Osamu Gotoh (1982). "An improved algorithm for matching biological sequences". Journal of Molecular Biology. 162 (3): 705–708. CiteSeerX 10.1.1.204.203. doi:10.1016/0022-2836(82)90398-9. PMID 7166760.
Miller, Webb; Myers, Eugene (1988). "Optimal alignments in linear space". Bioinformatics. 4 (1): 11–17. CiteSeerX 10.1.1.107.6989. doi:10.1093/bioinformatics/4.1.11. PMID 3382986.
D. S. Hirschberg (1975). "A linear space algorithm for computing maximal common subsequences". Communications of the ACM. 18 (6): 341–343. CiteSeerX 10.1.1.348.4774. doi:10.1145/360825.360861. S2CID 207694727.

semanticscholar.org

api.semanticscholar.org

Stephen F. Altschul & Bruce W. Erickson (1986). "Optimal sequence alignment using affine gap costs". Bulletin of Mathematical Biology. 48 (5–6): 603–616. doi:10.1007/BF02462326. PMID 3580642. S2CID 189889143.
Chowdhury, Rezaul; Le, Hai-Son; Ramachandran, Vijaya (July 2010). "Cache-oblivious dynamic programming for bioinformatics". IEEE/ACM Transactions on Computational Biology and Bioinformatics. 7 (3): 495–510. doi:10.1109/TCBB.2008.94. PMID 20671320. S2CID 2532039.
D. S. Hirschberg (1975). "A linear space algorithm for computing maximal common subsequences". Communications of the ACM. 18 (6): 341–343. CiteSeerX 10.1.1.348.4774. doi:10.1145/360825.360861. S2CID 207694727.

tudelft.nl

repository.tudelft.nl

Vermij, Erik (2011). Genetic sequence alignment on a supercomputing platform (PDF) (M.Sc. thesis). Delft University of Technology. Archived from the original (PDF) on 2011-09-30. Retrieved 2011-08-17.

usc.edu

dornsife.usc.edu

Smith, Temple F. & Waterman, Michael S. (1981). "Identification of Common Molecular Subsequences" (PDF). Journal of Molecular Biology. 147 (1): 195–197. CiteSeerX 10.1.1.63.2897. doi:10.1016/0022-2836(81)90087-5. PMID 7265238.

web.archive.org

FPGA 100x Papers: "Archived copy" (PDF). Archived from the original (PDF) on 2008-07-05. Retrieved 2007-10-17.{{cite web}}: CS1 maint: archived copy as title (link), "Archived copy" (PDF). Archived from the original (PDF) on 2008-07-05. Retrieved 2007-10-17.{{cite web}}: CS1 maint: archived copy as title (link), and "Archived copy" (PDF). Archived from the original (PDF) on 2011-07-20. Retrieved 2007-10-17.{{cite web}}: CS1 maint: archived copy as title (link)
Vermij, Erik (2011). Genetic sequence alignment on a supercomputing platform (PDF) (M.Sc. thesis). Delft University of Technology. Archived from the original (PDF) on 2011-09-30. Retrieved 2011-08-17.
"Bioinformatics High Throughput Sequence Search and Analysis (white paper)". GenomeQuest. Archived from the original on May 13, 2008. Retrieved 2008-05-09.