List of sequence alignment software (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "List of sequence alignment software" in English language version.

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75nih.gov

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55doi.org

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6harvard.edu

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5handle.net

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1github.com

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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ; Gish; Miller; Myers; Lipman (October 1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–10. doi:10.1016/S0022-2836(05)80360-2. PMID 2231712. S2CID 14441902.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Angermüller, C.; Biegert, A.; Söding, J. (Dec 2012). "Discriminative modelling of context-specific amino acid substitution probabilities". Bioinformatics. 28 (24): 3240–7. doi:10.1093/bioinformatics/bts622. hdl:11858/00-001M-0000-0015-8D22-F. PMID 23080114.
Buchfink, Xie and Huson (2015). "Fast and sensitive protein alignment using DIAMOND". Nature Methods. 12 (1): 59–60. doi:10.1038/nmeth.3176. PMID 25402007. S2CID 5346781.
B Buchfink, K Reuter and HG Drost (2021). "Sensitive protein alignments at tree-of-life scale using DIAMOND". Nature Methods. 18 (4): 366–368. doi:10.1038/s41592-021-01101-x. PMC 8026399. PMID 33828273.
Söding J (April 2005). "Protein homology detection by HMM-HMM comparison". Bioinformatics. 21 (7): 951–60. doi:10.1093/bioinformatics/bti125. hdl:11858/00-001M-0000-0017-EC7A-F. PMID 15531603.
Remmert, Michael; Biegert, Andreas; Hauser, Andreas; Söding, Johannes (2011-12-25). "HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment". Nature Methods. 9 (2): 173–175. doi:10.1038/nmeth.1818. hdl:11858/00-001M-0000-0015-8D56-A. ISSN 1548-7105. PMID 22198341. S2CID 205420247.
Hauswedell H, Singer J, Reinert K (2014-09-01). "Lambda: the local aligner for massive biological data". Bioinformatics. 30 (17): 349–355. doi:10.1093/bioinformatics/btu439. PMC 4147892. PMID 25161219.
Steinegger, Martin; Soeding, Johannes (2017-10-16). "MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets". Nature Biotechnology. 35 (11): 1026–1028. doi:10.1038/nbt.3988. hdl:11858/00-001M-0000-002E-1967-3. PMID 29035372. S2CID 402352.
Rucci, Enzo; Garcia, Carlos; Botella, Guillermo; Giusti, Armando E. De; Naiouf, Marcelo; Prieto-Matias, Manuel (2016-06-30). "OSWALD: OpenCL Smith–Waterman on Altera's FPGA for Large Protein Databases". International Journal of High Performance Computing Applications. 32 (3): 337–350. doi:10.1177/1094342016654215. ISSN 1094-3420. S2CID 212680914.
Altschul SF, Madden TL, Schäffer AA, et al. (September 1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 (17): 3389–402. doi:10.1093/nar/25.17.3389. PMC 146917. PMID 9254694.
Li W, McWilliam H, Goujon M, et al. (June 2012). "PSI-Search: iterative HOE-reduced profile SSEARCH searching". Bioinformatics. 28 (12): 1650–1651. doi:10.1093/bioinformatics/bts240. PMC 3371869. PMID 22539666.
Oehmen, C.; Nieplocha, J. (August 2006). "ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis". IEEE Transactions on Parallel and Distributed Systems. 17 (8): 740–749. doi:10.1109/TPDS.2006.112. S2CID 11122366.
Rucci, Enzo; García, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto-Matías, Manuel (2015-12-25). "An energy-aware performance analysis of SWIMM: Smith–Waterman implementation on Intel's Multicore and Manycore architectures". Concurrency and Computation: Practice and Experience. 27 (18): 5517–5537. doi:10.1002/cpe.3598. hdl:11336/53930. ISSN 1532-0634. S2CID 42945406.
Rucci, Enzo; García, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto-Matías, Manuel (2015-12-25). "SWIMM 2.0: enhanced Smith-Waterman on Intel's Multicore and Manycore architectures based on AVX-512 vector extensions". International Journal of Parallel Programming. 47 (2): 296–317. doi:10.1007/s10766-018-0585-7. ISSN 1573-7640. S2CID 49670113.
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W; Kent; Smit; Zhang; Baertsch; Hardison; Haussler; Miller (2003). "Human-mouse alignments with BLASTZ". Genome Research. 13 (1): 103–107. doi:10.1101/gr.809403. PMC 430961. PMID 12529312.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Sandes, Edans F. de O.; de Melo, Alba Cristina M.A. (May 2013). "Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences Using GPU". IEEE Transactions on Parallel and Distributed Systems. 24 (5): 1009–1021. doi:10.1109/TPDS.2012.194.
Sandes, Edans F. de O.; Miranda, G.; De Melo, A.C.M.A.; Martorell, X.; Ayguade, E. (May 2014). CUDAlign 3.0: Parallel Biological Sequence Comparison in Large GPU Clusters. Cluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on. p. 160. doi:10.1109/CCGrid.2014.18.
Sandes, Edans F. de O.; Miranda, G.; De Melo, A.C.M.A.; Martorell, X.; Ayguade, E. (August 2014). Fine-grain Parallel Megabase Sequence Comparison with Multiple Heterogeneous GPUs. Proceedings of the 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. pp. 383–384. doi:10.1145/2555243.2555280.
Chivian, D; Baker, D (2006). "Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection". Nucleic Acids Research. 34 (17): e112. doi:10.1093/nar/gkl480. PMC 1635247. PMID 16971460.
Girdea, M; Noe, L; Kucherov, G (January 2010). "Back-translation for discovering distant protein homologies in the presence of frameshift mutations". Algorithms for Molecular Biology. 5 (6): 6. doi:10.1186/1748-7188-5-6. PMC 2821327. PMID 20047662.
Ma, B.; Tromp, J.; Li, M. (2002). "PatternHunter: faster and more sensitive homology search". Bioinformatics. 18 (3): 440–445. doi:10.1093/bioinformatics/18.3.440. PMID 11934743.
Li, M.; Ma, B.; Kisman, D.; Tromp, J. (2004). "Patternhunter II: highly sensitive and fast homology search". Journal of Bioinformatics and Computational Biology. 2 (3): 417–439. CiteSeerX 10.1.1.1.2393. doi:10.1142/S0219720004000661. PMID 15359419.
Rucci, Enzo; Garcia, Carlos; Botella, Guillermo; Naiouf, Marcelo; De Giusti,Armando; Prieto-Matias, Manuel (2018). "SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences". BMC Systems Biology. 12 (Suppl 5): 96. doi:10.1186/s12918-018-0614-6. PMC 6245597. PMID 30458766.
Rucci, Enzo; Garcia, Carlos; Botella, Guillermo; Naiouf, Marcelo; De Giusti,Armando; Prieto-Matias, Manuel. Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA. 5th International Work-Conference on Bioinformatics and Biomedical Engineering. pp. 500–511. doi:10.1007/978-3-319-56154-7_45.
Rasmussen K, Stoye J, Myers EW; Stoye; Myers (2006). "Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length". Journal of Computational Biology. 13 (2): 296–308. CiteSeerX 10.1.1.465.2084. doi:10.1089/cmb.2006.13.296. PMID 16597241.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Noe L, Kucherov G; Kucherov (2005). "YASS: enhancing the sensitivity of DNA similarity search". Nucleic Acids Research. 33 (suppl_2): W540–W543. doi:10.1093/nar/gki478. PMC 1160238. PMID 15980530.
Pratas, Diogo; Silva, Jorge (2020). "Persistent minimal sequences of SARS-CoV-2". Bioinformatics. 36 (21): 5129–5132. doi:10.1093/bioinformatics/btaa686. PMC 7559010. PMID 32730589.
Wilton, Richard; Budavari, Tamas; Langmead, Ben; Wheelan, Sarah J.; Salzberg, Steven L.; Szalay, Alexander S. (2015). "Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space". PeerJ. 3: e808. doi:10.7717/peerj.808. PMC 4358639. PMID 25780763.
Homer, Nils; Merriman, Barry; Nelson, Stanley F. (2009). "BFAST: An Alignment Tool for Large Scale Genome Resequencing". PLOS ONE. 4 (11): e7767. Bibcode:2009PLoSO...4.7767H. doi:10.1371/journal.pone.0007767. PMC 2770639. PMID 19907642.
Abuín, J.M.; Pichel, J.C.; Pena, T.F.; Amigo, J. (2015). "BigBWA: approaching the Burrows–Wheeler aligner to Big Data technologies". Bioinformatics. 31 (24): 4003–5. doi:10.1093/bioinformatics/btv506. PMID 26323715.
Kent, W. J. (2002). "BLAT---The BLAST-Like Alignment Tool". Genome Research. 12 (4): 656–664. doi:10.1101/gr.229202. ISSN 1088-9051. PMC 187518. PMID 11932250.
Langmead, Ben; Trapnell, Cole; Pop, Mihai; Salzberg, Steven L (2009). "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome". Genome Biology. 10 (3): R25. doi:10.1186/gb-2009-10-3-r25. ISSN 1465-6906. PMC 2690996. PMID 19261174.
Li, H.; Durbin, R. (2009). "Fast and accurate short read alignment with Burrows–Wheeler transform". Bioinformatics. 25 (14): 1754–1760. doi:10.1093/bioinformatics/btp324. ISSN 1367-4803. PMC 2705234. PMID 19451168.
Kerpedjiev, Peter; Frellsen, Jes; Lindgreen, Stinus; Krogh, Anders (2014). "Adaptable probabilistic mapping of short reads using position specific scoring matrices". BMC Bioinformatics. 15 (1): 100. doi:10.1186/1471-2105-15-100. ISSN 1471-2105. PMC 4021105. PMID 24717095.
Liu, Y.; Schmidt, B.; Maskell, D. L. (2012). "CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform". Bioinformatics. 28 (14): 1830–1837. doi:10.1093/bioinformatics/bts276. ISSN 1367-4803. PMID 22576173.
Liu, Y.; Schmidt, B. (2012). "Long read alignment based on maximal exact match seeds". Bioinformatics. 28 (18): i318–i324. doi:10.1093/bioinformatics/bts414. ISSN 1367-4803. PMC 3436841. PMID 22962447.
Rizk, Guillaume; Lavenier, Dominique (2010). "GASSST: global alignment short sequence search tool". Bioinformatics. 26 (20): 2534–2540. doi:10.1093/bioinformatics/btq485. PMC 2951093. PMID 20739310.
Marco-Sola, Santiago; Sammeth, Michael; Guigó, Roderic; Ribeca, Paolo (2012). "The GEM mapper: fast, accurate and versatile alignment by filtration". Nature Methods. 9 (12): 1185–1188. doi:10.1038/nmeth.2221. ISSN 1548-7091. PMID 23103880. S2CID 2004416.
Clement, N. L.; Snell, Q.; Clement, M. J.; Hollenhorst, P. C.; Purwar, J.; Graves, B. J.; Cairns, B. R.; Johnson, W. E. (2009). "The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing". Bioinformatics. 26 (1): 38–45. doi:10.1093/bioinformatics/btp614. ISSN 1367-4803. PMC 6276904. PMID 19861355.
Santana-Quintero, Luis; Dingerdissen, Hayley; Thierry-Mieg, Jean; Mazumder, Raja; Simonyan, Vahan (2014). "HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis". PLOS ONE. 9 (6): 1754–1760. Bibcode:2014PLoSO...999033S. doi:10.1371/journal.pone.0099033. PMC 4053384. PMID 24918764.
Kielbasa, S.M.; Wan, R.; Sato, K.; Horton, P.; Frith, M.C. (2011). "Adaptive seeds tame genomic sequence comparison". Genome Research. 21 (3): 487–493. doi:10.1101/gr.113985.110. PMC 3044862. PMID 21209072.
Rivals, Eric; Salmela, Leena; Kiiskinen, Petteri; Kalsi, Petri; Tarhio, Jorma (2009). "Mpscan: Fast Localisation of Multiple Reads in Genomes". Algorithms in Bioinformatics. Lecture Notes in Computer Science. Vol. 5724. pp. 246–260. Bibcode:2009LNCS.5724..246R. CiteSeerX 10.1.1.156.928. doi:10.1007/978-3-642-04241-6_21. ISBN 978-3-642-04240-9. S2CID 17187140.
Sedlazeck, Fritz J.; Rescheneder, Philipp; von Haeseler, Arndt (2013). "NextGenMap: fast and accurate read mapping in highly polymorphic genomes". Bioinformatics. 29 (21): 2790–2791. doi:10.1093/bioinformatics/btt468. PMID 23975764.
Chen, Yangho; Souaiaia, Tade; Chen, Ting (2009). "PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds". Bioinformatics. 25 (19): 2514–2521. doi:10.1093/bioinformatics/btp486. PMC 2752623. PMID 19675096.
Searls, David B.; Hoffmann, Steve; Otto, Christian; Kurtz, Stefan; Sharma, Cynthia M.; Khaitovich, Philipp; Vogel, Jörg; Stadler, Peter F.; Hackermüller, Jörg (2009). "Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures". PLOS Computational Biology. 5 (9): e1000502. Bibcode:2009PLSCB...5E0502H. doi:10.1371/journal.pcbi.1000502. ISSN 1553-7358. PMC 2730575. PMID 19750212.
Rumble, Stephen M.; Lacroute, Phil; Dalca, Adrian V.; Fiume, Marc; Sidow, Arend; Brudno, Michael (2009). "SHRiMP: Accurate Mapping of Short Color-space Reads". PLOS Computational Biology. 5 (5): e1000386. Bibcode:2009PLSCB...5E0386R. doi:10.1371/journal.pcbi.1000386. PMC 2678294. PMID 19461883.
David, Matei; Dzamba, Misko; Lister, Dan; Ilie, Lucian; Brudno, Michael (2011). "SHRiMP2: Sensitive yet Practical Short Read Mapping". Bioinformatics. 27 (7): 1011–1012. doi:10.1093/bioinformatics/btr046. PMID 21278192.
Malhis, Nawar; Butterfield, Yaron S. N.; Ester, Martin; Jones, Steven J. M. (2009). "Slider – Maximum use of probability information for alignment of short sequence reads and SNP detection". Bioinformatics. 25 (1): 6–13. doi:10.1093/bioinformatics/btn565. PMC 2638935. PMID 18974170.
Malhis, Nawar; Jones, Steven J. M. (2010). "High Quality SNP Calling Using Illumina Data at Shallow Coverage". Bioinformatics. 26 (8): 1029–1035. doi:10.1093/bioinformatics/btq092. PMID 20190250.
Li, R.; Li, Y.; Kristiansen, K.; Wang, J. (2008). "SOAP: short oligonucleotide alignment program". Bioinformatics. 24 (5): 713–714. doi:10.1093/bioinformatics/btn025. ISSN 1367-4803. PMID 18227114.
Li, R.; Yu, C.; Li, Y.; Lam, T.-W.; Yiu, S.-M.; Kristiansen, K.; Wang, J. (2009). "SOAP2: an improved ultrafast tool for short read alignment". Bioinformatics. 25 (15): 1966–1967. doi:10.1093/bioinformatics/btp336. ISSN 1367-4803. PMID 19497933.
Abuín, José M.; Pichel, Juan C.; Pena, Tomás F.; Amigo, Jorge (2016-05-16). "SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data". PLOS ONE. 11 (5): e0155461. Bibcode:2016PLoSO..1155461A. doi:10.1371/journal.pone.0155461. ISSN 1932-6203. PMC 4868289. PMID 27182962.
Lunter, G.; Goodson, M. (2010). "Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads". Genome Research. 21 (6): 936–939. doi:10.1101/gr.111120.110. ISSN 1088-9051. PMC 3106326. PMID 20980556.
Noe, L.; Girdea, M.; Kucherov, G. (2010). "Designing efficient spaced seeds for SOLiD read mapping". Advances in Bioinformatics. 2010: 708501. doi:10.1155/2010/708501. PMC 2945724. PMID 20936175.
Lin, H.; Zhang, Z.; Zhang, M.Q.; Ma, B.; Li, M. (2008). "ZOOM! Zillions of oligos mapped". Bioinformatics. 24 (21): 2431–2437. doi:10.1093/bioinformatics/btn416. PMC 2732274. PMID 18684737.

github.com

HPC-BLAST code repository https://github.com/UTennessee-JICS/HPC-BLAST

handle.net

hdl.handle.net

Angermüller, C.; Biegert, A.; Söding, J. (Dec 2012). "Discriminative modelling of context-specific amino acid substitution probabilities". Bioinformatics. 28 (24): 3240–7. doi:10.1093/bioinformatics/bts622. hdl:11858/00-001M-0000-0015-8D22-F. PMID 23080114.
Söding J (April 2005). "Protein homology detection by HMM-HMM comparison". Bioinformatics. 21 (7): 951–60. doi:10.1093/bioinformatics/bti125. hdl:11858/00-001M-0000-0017-EC7A-F. PMID 15531603.
Remmert, Michael; Biegert, Andreas; Hauser, Andreas; Söding, Johannes (2011-12-25). "HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment". Nature Methods. 9 (2): 173–175. doi:10.1038/nmeth.1818. hdl:11858/00-001M-0000-0015-8D56-A. ISSN 1548-7105. PMID 22198341. S2CID 205420247.
Steinegger, Martin; Soeding, Johannes (2017-10-16). "MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets". Nature Biotechnology. 35 (11): 1026–1028. doi:10.1038/nbt.3988. hdl:11858/00-001M-0000-002E-1967-3. PMID 29035372. S2CID 402352.
Rucci, Enzo; García, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto-Matías, Manuel (2015-12-25). "An energy-aware performance analysis of SWIMM: Smith–Waterman implementation on Intel's Multicore and Manycore architectures". Concurrency and Computation: Practice and Experience. 27 (18): 5517–5537. doi:10.1002/cpe.3598. hdl:11336/53930. ISSN 1532-0634. S2CID 42945406.

harvard.edu

ui.adsabs.harvard.edu

Homer, Nils; Merriman, Barry; Nelson, Stanley F. (2009). "BFAST: An Alignment Tool for Large Scale Genome Resequencing". PLOS ONE. 4 (11): e7767. Bibcode:2009PLoSO...4.7767H. doi:10.1371/journal.pone.0007767. PMC 2770639. PMID 19907642.
Santana-Quintero, Luis; Dingerdissen, Hayley; Thierry-Mieg, Jean; Mazumder, Raja; Simonyan, Vahan (2014). "HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis". PLOS ONE. 9 (6): 1754–1760. Bibcode:2014PLoSO...999033S. doi:10.1371/journal.pone.0099033. PMC 4053384. PMID 24918764.
Rivals, Eric; Salmela, Leena; Kiiskinen, Petteri; Kalsi, Petri; Tarhio, Jorma (2009). "Mpscan: Fast Localisation of Multiple Reads in Genomes". Algorithms in Bioinformatics. Lecture Notes in Computer Science. Vol. 5724. pp. 246–260. Bibcode:2009LNCS.5724..246R. CiteSeerX 10.1.1.156.928. doi:10.1007/978-3-642-04241-6_21. ISBN 978-3-642-04240-9. S2CID 17187140.
Searls, David B.; Hoffmann, Steve; Otto, Christian; Kurtz, Stefan; Sharma, Cynthia M.; Khaitovich, Philipp; Vogel, Jörg; Stadler, Peter F.; Hackermüller, Jörg (2009). "Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures". PLOS Computational Biology. 5 (9): e1000502. Bibcode:2009PLSCB...5E0502H. doi:10.1371/journal.pcbi.1000502. ISSN 1553-7358. PMC 2730575. PMID 19750212.
Rumble, Stephen M.; Lacroute, Phil; Dalca, Adrian V.; Fiume, Marc; Sidow, Arend; Brudno, Michael (2009). "SHRiMP: Accurate Mapping of Short Color-space Reads". PLOS Computational Biology. 5 (5): e1000386. Bibcode:2009PLSCB...5E0386R. doi:10.1371/journal.pcbi.1000386. PMC 2678294. PMID 19461883.
Abuín, José M.; Pichel, Juan C.; Pena, Tomás F.; Amigo, Jorge (2016-05-16). "SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data". PLOS ONE. 11 (5): e0155461. Bibcode:2016PLoSO..1155461A. doi:10.1371/journal.pone.0155461. ISSN 1932-6203. PMC 4868289. PMID 27182962.

nature.com

Steinegger, Martin; Soeding, Johannes (2017-10-16). "MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets". Nature Biotechnology. 35 (11): 1026–1028. doi:10.1038/nbt.3988. hdl:11858/00-001M-0000-002E-1967-3. PMID 29035372. S2CID 402352.

nih.gov

pubmed.ncbi.nlm.nih.gov

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ; Gish; Miller; Myers; Lipman (October 1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–10. doi:10.1016/S0022-2836(05)80360-2. PMID 2231712. S2CID 14441902.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Angermüller, C.; Biegert, A.; Söding, J. (Dec 2012). "Discriminative modelling of context-specific amino acid substitution probabilities". Bioinformatics. 28 (24): 3240–7. doi:10.1093/bioinformatics/bts622. hdl:11858/00-001M-0000-0015-8D22-F. PMID 23080114.
Buchfink, Xie and Huson (2015). "Fast and sensitive protein alignment using DIAMOND". Nature Methods. 12 (1): 59–60. doi:10.1038/nmeth.3176. PMID 25402007. S2CID 5346781.
B Buchfink, K Reuter and HG Drost (2021). "Sensitive protein alignments at tree-of-life scale using DIAMOND". Nature Methods. 18 (4): 366–368. doi:10.1038/s41592-021-01101-x. PMC 8026399. PMID 33828273.
Söding J (April 2005). "Protein homology detection by HMM-HMM comparison". Bioinformatics. 21 (7): 951–60. doi:10.1093/bioinformatics/bti125. hdl:11858/00-001M-0000-0017-EC7A-F. PMID 15531603.
Remmert, Michael; Biegert, Andreas; Hauser, Andreas; Söding, Johannes (2011-12-25). "HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment". Nature Methods. 9 (2): 173–175. doi:10.1038/nmeth.1818. hdl:11858/00-001M-0000-0015-8D56-A. ISSN 1548-7105. PMID 22198341. S2CID 205420247.
Hauswedell H, Singer J, Reinert K (2014-09-01). "Lambda: the local aligner for massive biological data". Bioinformatics. 30 (17): 349–355. doi:10.1093/bioinformatics/btu439. PMC 4147892. PMID 25161219.
Steinegger, Martin; Soeding, Johannes (2017-10-16). "MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets". Nature Biotechnology. 35 (11): 1026–1028. doi:10.1038/nbt.3988. hdl:11858/00-001M-0000-002E-1967-3. PMID 29035372. S2CID 402352.
Altschul SF, Madden TL, Schäffer AA, et al. (September 1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 (17): 3389–402. doi:10.1093/nar/25.17.3389. PMC 146917. PMID 9254694.
Li W, McWilliam H, Goujon M, et al. (June 2012). "PSI-Search: iterative HOE-reduced profile SSEARCH searching". Bioinformatics. 28 (12): 1650–1651. doi:10.1093/bioinformatics/bts240. PMC 3371869. PMID 22539666.
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W; Kent; Smit; Zhang; Baertsch; Hardison; Haussler; Miller (2003). "Human-mouse alignments with BLASTZ". Genome Research. 13 (1): 103–107. doi:10.1101/gr.809403. PMC 430961. PMID 12529312.{{cite journal}}: CS1 maint: multiple names: authors list (link)
Chivian, D; Baker, D (2006). "Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection". Nucleic Acids Research. 34 (17): e112. doi:10.1093/nar/gkl480. PMC 1635247. PMID 16971460.
Girdea, M; Noe, L; Kucherov, G (January 2010). "Back-translation for discovering distant protein homologies in the presence of frameshift mutations". Algorithms for Molecular Biology. 5 (6): 6. doi:10.1186/1748-7188-5-6. PMC 2821327. PMID 20047662.
Ma, B.; Tromp, J.; Li, M. (2002). "PatternHunter: faster and more sensitive homology search". Bioinformatics. 18 (3): 440–445. doi:10.1093/bioinformatics/18.3.440. PMID 11934743.
Li, M.; Ma, B.; Kisman, D.; Tromp, J. (2004). "Patternhunter II: highly sensitive and fast homology search". Journal of Bioinformatics and Computational Biology. 2 (3): 417–439. CiteSeerX 10.1.1.1.2393. doi:10.1142/S0219720004000661. PMID 15359419.
Rucci, Enzo; Garcia, Carlos; Botella, Guillermo; Naiouf, Marcelo; De Giusti,Armando; Prieto-Matias, Manuel (2018). "SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences". BMC Systems Biology. 12 (Suppl 5): 96. doi:10.1186/s12918-018-0614-6. PMC 6245597. PMID 30458766.
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ncbi.nlm.nih.gov

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psu.edu

citeseerx.ist.psu.edu

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sagepub.com

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ucsc.edu

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unlp.edu.ar

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Rucci, Enzo; García, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto-Matías, Manuel (2015-12-25). "An energy-aware performance analysis of SWIMM: Smith–Waterman implementation on Intel's Multicore and Manycore architectures". Concurrency and Computation: Practice and Experience. 27 (18): 5517–5537. doi:10.1002/cpe.3598. hdl:11336/53930. ISSN 1532-0634. S2CID 42945406.
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worldcat.org

Remmert, Michael; Biegert, Andreas; Hauser, Andreas; Söding, Johannes (2011-12-25). "HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment". Nature Methods. 9 (2): 173–175. doi:10.1038/nmeth.1818. hdl:11858/00-001M-0000-0015-8D56-A. ISSN 1548-7105. PMID 22198341. S2CID 205420247.
Rucci, Enzo; Garcia, Carlos; Botella, Guillermo; Giusti, Armando E. De; Naiouf, Marcelo; Prieto-Matias, Manuel (2016-06-30). "OSWALD: OpenCL Smith–Waterman on Altera's FPGA for Large Protein Databases". International Journal of High Performance Computing Applications. 32 (3): 337–350. doi:10.1177/1094342016654215. ISSN 1094-3420. S2CID 212680914.
Rucci, Enzo; García, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto-Matías, Manuel (2015-12-25). "An energy-aware performance analysis of SWIMM: Smith–Waterman implementation on Intel's Multicore and Manycore architectures". Concurrency and Computation: Practice and Experience. 27 (18): 5517–5537. doi:10.1002/cpe.3598. hdl:11336/53930. ISSN 1532-0634. S2CID 42945406.
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