Journal articles on the topic 'Sequence alignment algorithms'
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Cavanaugh, David, and Krishnan Chittur. "A hydrophobic proclivity index for protein alignments." F1000Research 4 (October 21, 2015): 1097. http://dx.doi.org/10.12688/f1000research.6348.1.
Full textCavanaugh, David, and Krishnan Chittur. "A hydrophobic proclivity index for protein alignments." F1000Research 4 (October 15, 2020): 1097. http://dx.doi.org/10.12688/f1000research.6348.2.
Full textArenas-Díaz, Edgar D., Helga Ochoterena, and Katya Rodríguez-Vázquez. "Multiple Sequence Alignment Using a Genetic Algorithm and GLOCSA." Journal of Artificial Evolution and Applications 2009 (August 27, 2009): 1–10. http://dx.doi.org/10.1155/2009/963150.
Full textWANG, YI, and KUO-BIN LI. "MULTIPLE SEQUENCE ALIGNMENT USING AN EXHAUSTIVE AND GREEDY ALGORITHM." Journal of Bioinformatics and Computational Biology 03, no. 02 (April 2005): 243–55. http://dx.doi.org/10.1142/s021972000500103x.
Full textBACKOFEN, ROLF, and SEBASTIAN WILL. "LOCAL SEQUENCE-STRUCTURE MOTIFS IN RNA." Journal of Bioinformatics and Computational Biology 02, no. 04 (December 2004): 681–98. http://dx.doi.org/10.1142/s0219720004000818.
Full textRautiainen, Mikko, Veli Mäkinen, and Tobias Marschall. "Bit-parallel sequence-to-graph alignment." Bioinformatics 35, no. 19 (March 9, 2019): 3599–607. http://dx.doi.org/10.1093/bioinformatics/btz162.
Full textCHIN, FRANCIS Y. L., N. L. HO, T. W. LAM, and PRUDENCE W. H. WONG. "EFFICIENT CONSTRAINED MULTIPLE SEQUENCE ALIGNMENT WITH PERFORMANCE GUARANTEE." Journal of Bioinformatics and Computational Biology 03, no. 01 (February 2005): 1–18. http://dx.doi.org/10.1142/s0219720005000977.
Full textZhu, J., J. S. Liu, and C. E. Lawrence. "Bayesian adaptive sequence alignment algorithms." Bioinformatics 14, no. 1 (February 1, 1998): 25–39. http://dx.doi.org/10.1093/bioinformatics/14.1.25.
Full textNARIMANI, ZAHRA, HAMID BEIGY, and HASSAN ABOLHASSANI. "A NEW GENETIC ALGORITHM FOR MULTIPLE SEQUENCE ALIGNMENT." International Journal of Computational Intelligence and Applications 11, no. 04 (December 2012): 1250023. http://dx.doi.org/10.1142/s146902681250023x.
Full textLong, Hai Xia, Li Hua Wu, and Yu Zhang. "Multiple Sequence Alignment Based on Profile Hidden Markov Model and Quantum-Behaved Particle Swarm Optimization with Selection Method." Advanced Materials Research 282-283 (July 2011): 7–12. http://dx.doi.org/10.4028/www.scientific.net/amr.282-283.7.
Full textKeith, Jonathan M., Peter Adams, Darryn Bryant, Keith R. Mitchelson, Duncan A. E. Cochran, and Gita H. Lala. "Inferring an Original Sequence from Erroneous Copies: Two Approaches." Asia-Pacific Biotech News 07, no. 03 (February 3, 2003): 107–14. http://dx.doi.org/10.1142/s0219030303000284.
Full textGambin, Anna, and Rafał Otto. "Contextual Multiple Sequence Alignment." Journal of Biomedicine and Biotechnology 2005, no. 2 (2005): 124–31. http://dx.doi.org/10.1155/jbb.2005.124.
Full textMd Isa, Mohd Nazrin, Sohiful Anuar Zainol Murad, Mohamad Imran Ahmad, Muhammad M. Ramli, and Rizalafande Che Ismail. "An Efficient Scheduling Technique for Biological Sequence Alignment." Applied Mechanics and Materials 754-755 (April 2015): 1087–92. http://dx.doi.org/10.4028/www.scientific.net/amm.754-755.1087.
Full textManavalan, Mani. "Fast Model-based Protein Homology Discovery without Alignment." Asia Pacific Journal of Energy and Environment 1, no. 2 (December 31, 2014): 169–84. http://dx.doi.org/10.18034/apjee.v1i2.580.
Full textBarton, Geoffrey J. "Protein Sequence Alignment Techniques." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 1998): 1139–46. http://dx.doi.org/10.1107/s0907444998008324.
Full textFang, Meng, Jiawei Xu, Nan Sun, and Stephen S. T. Yau. "Generating Minimal Models of H1N1 NS1 Gene Sequences Using Alignment-Based and Alignment-Free Algorithms." Genes 14, no. 1 (January 10, 2023): 186. http://dx.doi.org/10.3390/genes14010186.
Full textPENG, YUNG-HSING, CHANG-BIAU YANG, KUO-TSUNG TSENG, and KUO-SI HUANG. "AN ALGORITHM AND APPLICATIONS TO SEQUENCE ALIGNMENT WITH WEIGHTED CONSTRAINTS." International Journal of Foundations of Computer Science 21, no. 01 (February 2010): 51–59. http://dx.doi.org/10.1142/s012905411000712x.
Full textGOTOH, O. "Multiple sequence alignment: Algorithms and applications." Advances in Biophysics 36 (1999): 159–206. http://dx.doi.org/10.1016/s0065-227x(99)80007-0.
Full textBafna, Vineet, Eugene L. Lawler, and Pavel A. Pevzner. "Approximation algorithms for multiple sequence alignment." Theoretical Computer Science 182, no. 1-2 (August 1997): 233–44. http://dx.doi.org/10.1016/s0304-3975(97)00023-6.
Full textPinhas, Tamar, Nimrod Milo, Gregory Kucherov, and Michal Ziv-Ukelson. "Algorithms for path-constrained sequence alignment." Journal of Discrete Algorithms 24 (January 2014): 48–58. http://dx.doi.org/10.1016/j.jda.2013.09.003.
Full textWaterman, Michael S. "Parametric and ensemble sequence alignment algorithms." Bulletin of Mathematical Biology 56, no. 4 (July 1994): 743–67. http://dx.doi.org/10.1007/bf02460719.
Full textWATERMAN, M. "Parametric and ensemble sequence alignment algorithms." Bulletin of Mathematical Biology 56, no. 4 (July 1994): 743–67. http://dx.doi.org/10.1016/s0092-8240(05)80311-8.
Full textJiang, Yihang, Yuankai Qi, Will Ke Wang, Brinnae Bent, Robert Avram, Jeffrey Olgin, and Jessilyn Dunn. "EventDTW: An Improved Dynamic Time Warping Algorithm for Aligning Biomedical Signals of Nonuniform Sampling Frequencies." Sensors 20, no. 9 (May 9, 2020): 2700. http://dx.doi.org/10.3390/s20092700.
Full textWojciechowski, Pawel, Wojciech Frohmberg, Michal Kierzynka, Piotr Zurkowski, and Jacek Blazewicz. "G-MAPSEQ – a new method for mapping reads to a reference genome." Foundations of Computing and Decision Sciences 41, no. 2 (June 1, 2016): 123–42. http://dx.doi.org/10.1515/fcds-2016-0007.
Full textAlser, Mohammed, Hasan Hassan, Akash Kumar, Onur Mutlu, and Can Alkan. "Shouji: a fast and efficient pre-alignment filter for sequence alignment." Bioinformatics 35, no. 21 (March 28, 2019): 4255–63. http://dx.doi.org/10.1093/bioinformatics/btz234.
Full textDaugelaite, Jurate, Aisling O' Driscoll, and Roy D. Sleator. "An Overview of Multiple Sequence Alignments and Cloud Computing in Bioinformatics." ISRN Biomathematics 2013 (August 14, 2013): 1–14. http://dx.doi.org/10.1155/2013/615630.
Full textWANG, ZHUOZHI, and KAIZHONG ZHANG. "MULTIPLE RNA STRUCTURE ALIGNMENT." Journal of Bioinformatics and Computational Biology 03, no. 03 (June 2005): 609–26. http://dx.doi.org/10.1142/s0219720005001296.
Full textSpirollari, Junilda, Jason T. L. Wang, Kaizhong Zhang, Vivian Bellofatto, Yongkyu Park, and Bruce A. Shapiro. "Predicting Consensus Structures for RNA Alignments via Pseudo-Energy Minimization." Bioinformatics and Biology Insights 3 (January 2009): BBI.S2578. http://dx.doi.org/10.4137/bbi.s2578.
Full textChao, Jiannan, Furong Tang, and Lei Xu. "Developments in Algorithms for Sequence Alignment: A Review." Biomolecules 12, no. 4 (April 6, 2022): 546. http://dx.doi.org/10.3390/biom12040546.
Full textWilburn, Grey W., and Sean R. Eddy. "Remote homology search with hidden Potts models." PLOS Computational Biology 16, no. 11 (November 30, 2020): e1008085. http://dx.doi.org/10.1371/journal.pcbi.1008085.
Full textSauder, J. Michael, Jonathan W. Arthur, and Roland L. Dunbrack Jr. "Large-scale comparison of protein sequence alignment algorithms with structure alignments." Proteins: Structure, Function, and Genetics 40, no. 1 (July 1, 2000): 6–22. http://dx.doi.org/10.1002/(sici)1097-0134(20000701)40:1<6::aid-prot30>3.0.co;2-7.
Full textPaten, B., D. Earl, N. Nguyen, M. Diekhans, D. Zerbino, and D. Haussler. "Cactus: Algorithms for genome multiple sequence alignment." Genome Research 21, no. 9 (June 10, 2011): 1512–28. http://dx.doi.org/10.1101/gr.123356.111.
Full textShahab, Muhammad Luthfi, and Mohammad Isa Irawan. "Sequence Alignment Using Nature-Inspired Metaheuristic Algorithms." International Journal of Computing Science and Applied Mathematics 3, no. 1 (March 1, 2017): 27. http://dx.doi.org/10.12962/j24775401.v3i1.2118.
Full textNotredame, Cédric. "Recent Evolutions of Multiple Sequence Alignment Algorithms." PLoS Computational Biology 3, no. 8 (August 31, 2007): e123. http://dx.doi.org/10.1371/journal.pcbi.0030123.
Full textRangwala, H., and G. Karypis. "Incremental window-based protein sequence alignment algorithms." Bioinformatics 23, no. 2 (January 15, 2007): e17-e23. http://dx.doi.org/10.1093/bioinformatics/btl297.
Full textCatanach, Therese A., Andrew D. Sweet, Nam-phuong D. Nguyen, Rhiannon M. Peery, Andrew H. Debevec, Andrea K. Thomer, Amanda C. Owings, et al. "Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus." PeerJ 7 (January 3, 2019): e6142. http://dx.doi.org/10.7717/peerj.6142.
Full textSchroedl, S. "An Improved Search Algorithm for Optimal Multiple-Sequence Alignment." Journal of Artificial Intelligence Research 23 (May 1, 2005): 587–623. http://dx.doi.org/10.1613/jair.1534.
Full textKostenko, Dimitrii O., and Eugene V. Korotkov. "Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences." International Journal of Molecular Sciences 23, no. 7 (March 29, 2022): 3764. http://dx.doi.org/10.3390/ijms23073764.
Full textKalinin, M., and V. Krundyshev. "Sequence Alignment Algorithms for Intrusion Detection in the Internet of Things." Nonlinear Phenomena in Complex Systems 23, no. 4 (December 4, 2020): 397–404. http://dx.doi.org/10.33581/1561-4085-2020-23-4-397-404.
Full textZhan, Qing, Yilei Fu, Qinghua Jiang, Bo Liu, Jiajie Peng, and Yadong Wang. "SpliVert: A Protein Multiple Sequence Alignment Refinement Method Based on Splitting-Splicing Vertically." Protein & Peptide Letters 27, no. 4 (March 17, 2020): 295–302. http://dx.doi.org/10.2174/0929866526666190806143959.
Full textSilva, Fernando José Mateus da, Juan Manuel Sánchez Pérez, Juan Antonio Gómez Pulido, and Miguel A. Vega Rodríguez. "Parallel Niche Pareto AlineaGA – an Evolutionary Multiobjective approach on Multiple Sequence Alignment." Journal of Integrative Bioinformatics 8, no. 3 (December 1, 2011): 57–72. http://dx.doi.org/10.1515/jib-2011-174.
Full textGupta, Ruchi, and Pankaj Agarwal. "SOGA: space oriented genetic algorithm for multiple sequence alignment." International Journal of Engineering & Technology 7, no. 4.5 (September 22, 2018): 481. http://dx.doi.org/10.14419/ijet.v7i4.5.21138.
Full textSong, Yinglei, Chunmei Liu, Xiuzhen Huang, Russell Malmberg, Ying Xu, and Liming Cai. "Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment." IEEE/ACM Transactions on Computational Biology and Bioinformatics 3, no. 4 (October 2006): 423–32. http://dx.doi.org/10.1109/tcbb.2006.52.
Full textLiu Weiguo, B. Schmidt, G. Voss, and W. Muller-Wittig. "Streaming Algorithms for Biological Sequence Alignment on GPUs." IEEE Transactions on Parallel and Distributed Systems 18, no. 9 (September 2007): 1270–81. http://dx.doi.org/10.1109/tpds.2007.1069.
Full textChung, Yun-Sheng, Chin Lung Lu, and Chuan Yi Tang. "Efficient algorithms for regular expression constrained sequence alignment." Information Processing Letters 103, no. 6 (September 2007): 240–46. http://dx.doi.org/10.1016/j.ipl.2007.04.007.
Full textLe Thi, Hoai An, Tao Pham Dinh, and Moulay Belghiti. "DCA based algorithms for multiple sequence alignment (MSA)." Central European Journal of Operations Research 22, no. 3 (September 1, 2013): 501–24. http://dx.doi.org/10.1007/s10100-013-0324-5.
Full textBen Othman, Mohamed Tahar. "Survey of the use of genetic algorithm for multiple sequence alignment." Journal of Advanced Computer Science & Technology 5, no. 2 (June 8, 2016): 28. http://dx.doi.org/10.14419/jacst.v5i2.6079.
Full textHo, Jiacang, and Dae-Ki Kang. "Sequence Alignment with Dynamic Divisor Generation for Keystroke Dynamics Based User Authentication." Journal of Sensors 2015 (2015): 1–14. http://dx.doi.org/10.1155/2015/935986.
Full textLipták, Panna, Attila Kiss, and János Márk Szalai-Gindl. "Heuristic Pairwise Alignment in Database Environments." Genes 13, no. 11 (November 2, 2022): 2005. http://dx.doi.org/10.3390/genes13112005.
Full textKorotkov, Eugene V., Yulia M. Suvorova, Dmitrii O. Kostenko, and Maria A. Korotkova. "Multiple Alignment of Promoter Sequences from the Arabidopsis thaliana L. Genome." Genes 12, no. 2 (January 21, 2021): 135. http://dx.doi.org/10.3390/genes12020135.
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