{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T22:57:32Z","timestamp":1780441052269,"version":"3.54.1"},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2009,10,8]],"date-time":"2009-10-08T00:00:00Z","timestamp":1254960000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Sign Process Syst"],"published-print":{"date-parts":[[2010,11]]},"DOI":"10.1007\/s11265-009-0409-5","type":"journal-article","created":{"date-parts":[[2009,10,7]],"date-time":"2009-10-07T06:38:57Z","timestamp":1254897537000},"page":"117-125","source":"Crossref","is-referenced-by-count":4,"title":["Accelerating Scalar-Product Based Sequence Alignment using Graphics Processor Units"],"prefix":"10.1007","volume":"61","author":[{"given":"Cem Savas","family":"Bassoy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Svetlana","family":"Torgasin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mei","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karl-Heinz","family":"Zimmermann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2009,10,8]]},"reference":[{"key":"409_CR1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschult","year":"1990","unstructured":"Altschult, S. F., Gish, W., Miller, W., Meyers, E. W., Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403\u2013410.","journal-title":"Journal of Molecular Biology"},{"key":"409_CR2","doi-asserted-by":"crossref","DOI":"10.1007\/3-540-31619-1","volume-title":"Numerical solution of partial differential equations on parallel computers","author":"AM Bruaset","year":"2006","unstructured":"Bruaset, A. M., & Tveito, A. (2006). Numerical solution of partial differential equations on parallel computers. New York: Springer."},{"key":"409_CR3","doi-asserted-by":"crossref","unstructured":"Buck, I. (2007). GPU Computing: Programming a massively parallel processor. In Proc Int Symp Code Gen Opt, IEEE Comp Soc, Washington DC.","DOI":"10.1109\/CGO.2007.13"},{"issue":"13","key":"409_CR4","doi-asserted-by":"crossref","first-page":"3497","DOI":"10.1093\/nar\/gkg500","volume":"31","author":"R Chenna","year":"2003","unstructured":"Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G., et al. (2003). Multiple sequence alignment with the clustal series of programs. Nucleic Acids Research, 31(13), 3497\u20133500.","journal-title":"Nucleic Acids Research"},{"key":"409_CR5","unstructured":"NVidia: NVidia Compute Unified Device Architecture (CUDA) (2008). Programming guide, version 2.0."},{"key":"409_CR6","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological sequence analysis","author":"R Durban","year":"1998","unstructured":"Durban, R., Eddy, S. R., Krogh, A., Mitchison, G. (1998). Biological sequence analysis. Cambridge: Cambridge University Press."},{"key":"409_CR7","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1007\/BF02603120","volume":"25","author":"DF Feng","year":"1987","unstructured":"Feng, D. F., & Doolittle, R. F. (1987). Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal Of Molecular Evolution, 25, 351\u2013360.","journal-title":"Journal Of Molecular Evolution"},{"key":"409_CR8","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/0378-1119(88)90330-7","volume":"73","author":"DG Higgins","year":"1988","unstructured":"Higgins, D. G., & Sharp, P. M. (1988). Clustal: A package for performing multiple sequence alignments on a microcomputer. Gene, 73, 237\u2013244.","journal-title":"Gene"},{"key":"409_CR9","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511574931","volume-title":"Algorithms on strings, trees, and sequences","author":"D Gusfield","year":"1997","unstructured":"Gusfield, D. (1997). Algorithms on strings, trees, and sequences. Cambridge: Cambridge University Press."},{"issue":"2","key":"409_CR10","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1016\/j.jcp.2006.06.039","volume":"221","author":"Y Juekuan","year":"2007","unstructured":"Juekuan, Y., Yujuan, W., Yunfei, C. (2007). GPU accelerated molecular dynamics simulation of thermal conductivity. Journal of Computational Physics, 221(2), 799\u2013804.","journal-title":"Journal of Computational Physics"},{"key":"409_CR11","volume-title":"The encyclopedia of molecular biology","year":"1980","unstructured":"Kendrew, J. (Ed.) (1980). The encyclopedia of molecular biology. Oxford: Blackwell Sci."},{"issue":"Suppl 2","key":"409_CR12","first-page":"10","volume":"9","author":"SA Manavski","year":"2008","unstructured":"Manavski, S. A., & Valle, G. (2008). CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BioMed Central Bioinformatics, 9(Suppl 2), S10.","journal-title":"BioMed Central Bioinformatics"},{"key":"409_CR13","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman, S. B., & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino acid sequences. Journal of Molecular Biology, 48, 443\u2013453.","journal-title":"Journal of Molecular Biology"},{"issue":"1","key":"409_CR14","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","volume":"302","author":"C Notredame","year":"2000","unstructured":"Notredame, C., Higgins, D. G., Heringa, J. (2000). Tcoffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302(1), 205\u2013217.","journal-title":"Journal of Molecular Biology"},{"key":"409_CR15","doi-asserted-by":"crossref","first-page":"2444","DOI":"10.1073\/pnas.85.8.2444","volume":"85","author":"RW Pearson","year":"1988","unstructured":"Pearson, R. W., & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America, 85, 2444\u20132448.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"1","key":"409_CR16","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1111\/j.1467-8659.2007.01012.x","volume":"26","author":"JD Owens","year":"2007","unstructured":"Owens, J. D., Luebke, D., Govindaraju, N., Harris, M., Kr\u00fcger, J., Lefohn, A. E., et al. (2007). A survey of general-purpose computation on graphics hardware. Computer Graphics Forum, 26(1), 80\u2013113.","journal-title":"Computer Graphics Forum"},{"key":"409_CR17","first-page":"474","volume":"8","author":"MC Schatz","year":"2007","unstructured":"Schatz, M. C., Trapnell, C., Delcher, A. L., Varashney, A. (2007). High-throughput sequence alignment using graphics processing units. BioMed Central Bioinformatics, 8, 474.","journal-title":"BioMed Central Bioinformatics"},{"issue":"2","key":"409_CR18","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/nbt0207-149","volume":"25","author":"C Shaffer","year":"2007","unstructured":"Shaffer, C. (2007). Next generation sequencing outspaces expectations. Nature Biotechnology, 25(2), 149.","journal-title":"Nature Biotechnology"},{"key":"409_CR19","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"RT Smith","year":"1981","unstructured":"Smith, R. T., & Waterman, M. S. (1981). Identification of common molecular subsequences. Journal of Molecular Biology, 147, 195\u2013197.","journal-title":"Journal of Molecular Biology"},{"key":"409_CR20","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-6846-3","volume-title":"Introduction to computational biology","author":"MS Waterman","year":"1995","unstructured":"Waterman, M. S. (1995). Introduction to computational biology. London: Chapman & Hall."},{"key":"409_CR21","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4419-9210-9","volume-title":"Introduction to protein informatics","author":"K-H Zimmermann","year":"2003","unstructured":"Zimmermann, K.-H. (2003). Introduction to protein informatics. Norwell: Kluwer."}],"container-title":["Journal of Signal Processing Systems"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11265-009-0409-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s11265-009-0409-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11265-009-0409-5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,1]],"date-time":"2019-06-01T08:19:32Z","timestamp":1559377172000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s11265-009-0409-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10,8]]},"references-count":21,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2010,11]]}},"alternative-id":["409"],"URL":"https:\/\/doi.org\/10.1007\/s11265-009-0409-5","relation":{},"ISSN":["1939-8018","1939-8115"],"issn-type":[{"value":"1939-8018","type":"print"},{"value":"1939-8115","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10,8]]}}}