Journal articles on the topic 'Pairwise sequence alignment'
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Staritzbichler, René, Edoardo Sarti, Emily Yaklich, et al. "Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors." PLOS ONE 16, no. 4 (2021): e0239881. http://dx.doi.org/10.1371/journal.pone.0239881.
Full textLakshmi, Naga Jayaprada.Gavarraju, and Karteeka Pavan K. "Pairwise Sequence Alignment by Differential Evolutionary Algorithm with New Mutation Strategy." International Journal of Engineering and Advanced Technology (IJEAT) 9, no. 2 (2019): 445–53. https://doi.org/10.35940/ijeat.B3136.129219.
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 (2010): 51–59. http://dx.doi.org/10.1142/s012905411000712x.
Full textDeRonne, Kevin W., and George Karypis. "Pareto Optimal Pairwise Sequence Alignment." IEEE/ACM Transactions on Computational Biology and Bioinformatics 10, no. 2 (2013): 481–93. http://dx.doi.org/10.1109/tcbb.2013.2.
Full textSierk, Michael L., Michael E. Smoot, Ellen J. Bass, and William R. Pearson. "Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments." BMC Bioinformatics 11, no. 1 (2010): 146. http://dx.doi.org/10.1186/1471-2105-11-146.
Full textTyson, Hugh. "Relationships between amino acid sequences determined through optimum alignments, clustering, and specific distance patterns: application to a group of scorpion toxins." Genome 35, no. 2 (1992): 360–71. http://dx.doi.org/10.1139/g92-055.
Full textTaneda, Akito. "Multi-objective pairwise RNA sequence alignment." Bioinformatics 26, no. 19 (2010): 2383–90. http://dx.doi.org/10.1093/bioinformatics/btq439.
Full textLi, Junjie, Sanjay Ranka, and Sartaj Sahni. "Pairwise sequence alignment for very long sequences on GPUs." International Journal of Bioinformatics Research and Applications 10, no. 4/5 (2014): 345. http://dx.doi.org/10.1504/ijbra.2014.062989.
Full textAdi Sunarto, Asril, and Prajoko Prajoko. "NEEDLEMAN-WUNSCH AND SMITH-WATERMAN COMBINATIONS IN PAIRWISE ALIGNMENT." Jurnal Mnemonic 7, no. 2 (2024): 140–43. http://dx.doi.org/10.36040/mnemonic.v7i2.9501.
Full textLipták, Panna, Attila Kiss, and János Márk Szalai-Gindl. "Heuristic Pairwise Alignment in Database Environments." Genes 13, no. 11 (2022): 2005. http://dx.doi.org/10.3390/genes13112005.
Full textPujari, Jeevana Jyothi, and Karteeka Pavan Kanadam. "Semi Global Pairwise Sequence Alignment Using New Chromosome Structure Genetic Algorithm." Ingénierie des systèmes d information 27, no. 1 (2022): 67–74. http://dx.doi.org/10.18280/isi.270108.
Full textLailil, Muflikhah, and Santoso Edy. "Pairwise Sequence Alignment between HBV and HCC Using Modified Needleman-Wunsch Algorithm." TELKOMNIKA Telecommunication, Computing, Electronics and Control 15, no. 4 (2017): 1785–93. https://doi.org/10.12928/TELKOMNIKA.v15i4.5813.
Full textKONAGURTHU, ARUN SIDDHARTH, JAMES WHISSTOCK, and PETER J. STUCKEY. "PROGRESSIVE MULTIPLE ALIGNMENT USING SEQUENCE TRIPLET OPTIMIZATIONS AND THREE-RESIDUE EXCHANGE COSTS." Journal of Bioinformatics and Computational Biology 02, no. 04 (2004): 719–45. http://dx.doi.org/10.1142/s0219720004000831.
Full textBandyopadhyay, S., and R. Mitra. "A Parallel Pairwise Local Sequence Alignment Algorithm." IEEE Transactions on NanoBioscience 8, no. 2 (2009): 139–46. http://dx.doi.org/10.1109/tnb.2009.2019642.
Full textZhu, Xiangyuan, and Jian Li. "Chemical Reaction Optimization for Pairwise Sequence Alignment." Journal of Computational and Theoretical Nanoscience 12, no. 12 (2015): 5351–57. http://dx.doi.org/10.1166/jctn.2015.4526.
Full textTaylor, William Ramsay. "Multiple sequence alignment by a pairwise algorithm." Bioinformatics 3, no. 2 (1987): 81–87. http://dx.doi.org/10.1093/bioinformatics/3.2.81.
Full textMullan, Lisa. "Pairwise sequence alignment—it's all about us!" Briefings in Bioinformatics 7, no. 1 (2006): 113–15. http://dx.doi.org/10.1093/bib/bbk008.
Full textGonzález Laffitte, Marcos E., and Peter F. Stadler. "Progressive Multiple Alignment of Graphs." Algorithms 17, no. 3 (2024): 116. http://dx.doi.org/10.3390/a17030116.
Full textPiña, Johan S., Simon Orozco-Arias, Nicolas Tobón-Orozco, Leonardo Camargo-Forero, Reinel Tabares-Soto, and Romain Guyot. "G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era." Evolutionary Bioinformatics 19 (January 2023): 117693432211505. http://dx.doi.org/10.1177/11769343221150585.
Full textWilson, W. C. "Activity Pattern Analysis by Means of Sequence-Alignment Methods." Environment and Planning A: Economy and Space 30, no. 6 (1998): 1017–38. http://dx.doi.org/10.1068/a301017.
Full textWilburn, Grey W., and Sean R. Eddy. "Remote homology search with hidden Potts models." PLOS Computational Biology 16, no. 11 (2020): e1008085. http://dx.doi.org/10.1371/journal.pcbi.1008085.
Full textFareed, Zeinab A., Hoda M. O. Mokhtar, and Ahmed Ahmed. "Gpcodon Alignment: A Global Pairwise Codon Based Sequence Alignment Approach." International Journal of Database Management Systems 8, no. 1 (2016): 1–12. http://dx.doi.org/10.5121/ijdms.2016.8101.
Full textMontañola, Alberto, Concepció Roig, and Porfidio Hernández. "Efficient mapping of genomic sequences to optimize multiple pairwise alignment in hybrid cluster platforms." Journal of Integrative Bioinformatics 11, no. 3 (2014): 60–71. http://dx.doi.org/10.1515/jib-2014-251.
Full textAgung, Widyo Utomo, Ananta Kusuma Wisnu, and Wahjuni Sri. "Parallelization of Pairwise Alignment and Neighbor-Joining Algorithm in Progressive Multiple Sequence Alignment." Indonesian Journal of Electrical Engineering and Computer 9, no. 1 (2018): 234–42. https://doi.org/10.11591/ijeecs.v9.i1.pp234-242.
Full textYakovlev, P. A. "Fast trie-based method for multiple pairwise sequence alignment." Доклады Академии наук 484, no. 4 (2019): 401–4. http://dx.doi.org/10.31857/s0869-56524844401-404.
Full textAsare, James Owusu, Justice Kwame Appati, and Kwaku Darkwah. "Formulation and Analysis of Patterns in a Score Matrix for Global Sequence Alignment." International Journal of Mathematics and Mathematical Sciences 2020 (June 1, 2020): 1–9. http://dx.doi.org/10.1155/2020/3858057.
Full textLandan, Giddy, and Dan Graur. "Characterization of pairwise and multiple sequence alignment errors." Gene 441, no. 1-2 (2009): 141–47. http://dx.doi.org/10.1016/j.gene.2008.05.016.
Full textUtomo, Agung Widyo. "Parallelization of Pairwise Alignment and Neighbor-Joining Algorithm in Progressive Multiple Sequence Alignment." Indonesian Journal of Electrical Engineering and Computer Science 9, no. 1 (2018): 234. http://dx.doi.org/10.11591/ijeecs.v9.i1.pp234-242.
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 textZhang, Jikai, Haidong Lan, Yuandong Chan, Yuan Shang, Bertil Schmidt, and Weiguo Liu. "BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures." Bioinformatics 35, no. 13 (2018): 2306–8. http://dx.doi.org/10.1093/bioinformatics/bty930.
Full textVishnepolsky, Boris, and Malak Pirtskhalava. "ALIGN_MTX—An optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment." Computational Biology and Chemistry 33, no. 3 (2009): 235–38. http://dx.doi.org/10.1016/j.compbiolchem.2009.04.003.
Full textBarlowe, Scott, Heather B. Coan, and Robert T. Youker. "SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment." PeerJ 5 (June 27, 2017): e3492. http://dx.doi.org/10.7717/peerj.3492.
Full textIsa, M. N., K. Benkrid, and T. Clayton. "Efficient architecture and scheduling technique for pairwise sequence alignment." ACM SIGARCH Computer Architecture News 40, no. 4 (2012): 26–31. http://dx.doi.org/10.1145/2411116.2411121.
Full textYakovlev, P. A. "Fast Trie-Based Method for Multiple Pairwise Sequence Alignment." Doklady Mathematics 99, no. 1 (2019): 64–67. http://dx.doi.org/10.1134/s1064562419010198.
Full textAbedulridha, Sara Q., and Eman S. Al-Shamery. "Pairwise DNA Sequence Alignment Using Multi-Zone Genetic Algorithm." Journal of Computational and Theoretical Nanoscience 16, no. 3 (2019): 935–40. http://dx.doi.org/10.1166/jctn.2019.7978.
Full textAbbasi, M., L. Paquete, A. Liefooghe, M. Pinheiro, and P. Matias. "Improvements on bicriteria pairwise sequence alignment: algorithms and applications." Bioinformatics 29, no. 8 (2013): 996–1003. http://dx.doi.org/10.1093/bioinformatics/btt098.
Full textAskari Rad, Mahbubeh, Alibek Kruglikov, and Xuhua Xia. "Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences." Algorithms 17, no. 5 (2024): 205. http://dx.doi.org/10.3390/a17050205.
Full textTyson, Hugh. "Relationships, derived from optimum alignments, among amino acid sequences of plant peroxidases." Canadian Journal of Botany 70, no. 3 (1992): 543–56. http://dx.doi.org/10.1139/b92-069.
Full textLee, Sung Jong, Keehyoung Joo, Sangjin Sim, Juyong Lee, In-Ho Lee, and Jooyoung Lee. "CRFalign: A Sequence-Structure Alignment of Proteins Based on a Combination of HMM-HMM Comparison and Conditional Random Fields." Molecules 27, no. 12 (2022): 3711. http://dx.doi.org/10.3390/molecules27123711.
Full textZhao, Xing-Ming, Yiu-Ming Cheung, and De-Shuang Huang. "A Novel Markov Pairwise Protein Sequence Alignment Method for Sequence 665 Comparison." Protein & Peptide Letters 12, no. 7 (2005): 665–69. http://dx.doi.org/10.2174/0929866054696190.
Full textMatsumoto, Yuki, and Shota Nakamura. "qualign: solving sequence alignment based on quadratic unconstrained binary optimisation." EMBnet.journal 28 (March 8, 2023): e1020. http://dx.doi.org/10.14806/ej.28.0.1020.
Full textPATEL, VANDANABEN, JASON T. L. WANG, SHEFALI SETIA, ANURAG VERMA, CHARLES D. WARDEN, and KAIZHONG ZHANG. "ON COMPARING TWO STRUCTURED RNA MULTIPLE ALIGNMENTS." Journal of Bioinformatics and Computational Biology 08, no. 06 (2010): 967–80. http://dx.doi.org/10.1142/s021972001000504x.
Full textBACKOFEN, ROLF, and SEBASTIAN WILL. "LOCAL SEQUENCE-STRUCTURE MOTIFS IN RNA." Journal of Bioinformatics and Computational Biology 02, no. 04 (2004): 681–98. http://dx.doi.org/10.1142/s0219720004000818.
Full textXia, Xuhua. "Post-Alignment Adjustment and Its Automation." Genes 12, no. 11 (2021): 1809. http://dx.doi.org/10.3390/genes12111809.
Full textHavgaard, J. H., R. B. Lyngso, G. D. Stormo, and J. Gorodkin. "Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%." Bioinformatics 21, no. 9 (2005): 1815–24. http://dx.doi.org/10.1093/bioinformatics/bti279.
Full textSong, Yong-Joon, Dong Jin Ji, Hyein Seo, Gyu-Bum Han, and Dong-Ho Cho. "Pairwise Heuristic Sequence Alignment Algorithm Based on Deep Reinforcement Learning." IEEE Open Journal of Engineering in Medicine and Biology 2 (2021): 36–43. http://dx.doi.org/10.1109/ojemb.2021.3055424.
Full textKhaled, H., R. El Gohary, N. L. Badr, and H. M. Faheem. "Accelerating pairwise DNA Sequence Alignment using the CUDA compatible GPU." International Journal of Computer Applications 84, no. 1 (2013): 25–31. http://dx.doi.org/10.5120/14542-2619.
Full textComet, J. P., and J. Henry. "Pairwise sequence alignment using a PROSITE pattern-derived similarity score." Computers & Chemistry 26, no. 5 (2002): 421–36. http://dx.doi.org/10.1016/s0097-8485(02)00005-0.
Full textGarai, Gautam, and Biswanath Chowdhury. "A cascaded pairwise biomolecular sequence alignment technique using evolutionary algorithm." Information Sciences 297 (March 2015): 118–39. http://dx.doi.org/10.1016/j.ins.2014.11.009.
Full textLi, W., J. Wang, and J. A. Feng. "NdPASA: a pairwise sequence alignment server for distantly related proteins." Bioinformatics 21, no. 19 (2005): 3803–5. http://dx.doi.org/10.1093/bioinformatics/bti619.
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