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Journal articles on the topic 'Alignment algorithm'

Author: Grafiati

Published: 25 May 2024

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1

Hung, Che-Lun, and Yaw-Ling Lin. "Implementation of a Parallel Protein Structure Alignment Service on Cloud." International Journal of Genomics 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/439681.

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Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment a

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WANG, YI, and KUO-BIN LI. "MULTIPLE SEQUENCE ALIGNMENT USING AN EXHAUSTIVE AND GREEDY ALGORITHM." Journal of Bioinformatics and Computational Biology 03, no. 02 (2005): 243–55. http://dx.doi.org/10.1142/s021972000500103x.

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We describe an exhaustive and greedy algorithm for improving the accuracy of multiple sequence alignment. A simple progressive alignment approach is employed to provide initial alignments. The initial alignment is then iteratively optimized against an objective function. For any working alignment, the optimization involves three operations: insertions, deletions and shuffles of gaps. The optimization is exhaustive since the algorithm applies the above operations to all eligible positions of an alignment. It is also greedy since only the operation that gives the best improving objective score w

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Arenas-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.

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Algorithms that minimize putative synapomorphy in an alignment cannot be directly implemented since trivial cases with concatenated sequences would be selected because they would imply a minimum number of events to be explained (e.g., a single insertion/deletion would be required to explain divergence among two sequences). Therefore, indirect measures to approach parsimony need to be implemented. In this paper, we thoroughly present a Global Criterion for Sequence Alignment (GLOCSA) that uses a scoring function to globally rate multiple alignments aiming to produce matrices that minimize the n

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WANG, ZHUOZHI, and KAIZHONG ZHANG. "MULTIPLE RNA STRUCTURE ALIGNMENT." Journal of Bioinformatics and Computational Biology 03, no. 03 (2005): 609–26. http://dx.doi.org/10.1142/s0219720005001296.

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Ribonucleic Acid (RNA) structures can be viewed as a special kind of strings where characters in a string can bond with each other. The question of aligning two RNA structures has been studied for a while, and there are several successful algorithms that are based upon different models. In this paper, by adopting the model introduced in Wang and Zhang,19 we propose two algorithms to attack the question of aligning multiple RNA structures. Our methods are to reduce the multiple RNA structure alignment problem to the problem of aligning two RNA structure alignments. Meanwhile, we will show that

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BACKOFEN, 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.

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Ribonuclic acid (RNA) enjoys increasing interest in molecular biology; despite this interest fundamental algorithms are lacking, e.g. for identifying local motifs. As proteins, RNA molecules have a distinctive structure. Therefore, in addition to sequence information, structure plays an important part in assessing the similarity of RNAs. Furthermore, common sequence-structure features in two or several RNA molecules are often only spatially local, where possibly large parts of the molecules are dissimilar. Consequently, we address the problem of comparing RNA molecules by computing an optimal

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Mirzaei, Soraya, Jafar Razmara, and Shahriar Lotfi. "GADP-align: A genetic algorithm and dynamic programming-based method for structural alignment of proteins." BioImpacts 11, no. 4 (2020): 271–79. http://dx.doi.org/10.34172/bi.2021.37.

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Introduction: Similarity analysis of protein structure is considered as a fundamental step to give insight into the relationships between proteins. The primary step in structural alignment is looking for the optimal correspondence between residues of two structures to optimize the scoring function. An exhaustive search for finding such a correspondence between two structures is intractable. Methods: In this paper, a hybrid method is proposed, namely GADP-align, for pairwise protein structure alignment. The proposed method looks for an optimal alignment using a hybrid method based on a genetic

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Zhou, Bin, and Wei Wang. "Fast Compass Alignment Algorithm of FOG SINS under Sway Condition." Applied Mechanics and Materials 321-324 (June 2013): 2171–76. http://dx.doi.org/10.4028/www.scientific.net/amm.321-324.2171.

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Through research on initial alignment problem of fiber optic gyro SINS in the sway condition, this paper proposed a rapid compass alignment scheme with variable parameters, which can accomplish rapid initial alignment. Firstly, analysted SINS compass alignment principle, and gave a concrete realization method which has the same calculation procedure with full damping navigation algorithm. This method makes the alignment and navigation to use the same set of algorithms, and can effectively reduce algorithm complexity. Simulation and repeatedly sway test results show that the alignment algorithm

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Ravi, Sujith, and Kevin Knight. "Does GIZA++ Make Search Errors?" Computational Linguistics 36, no. 3 (2010): 295–302. http://dx.doi.org/10.1162/coli_a_00008.

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Word alignment is a critical procedure within statistical machine translation (SMT). Brown et al. (1993) have provided the most popular word alignment algorithm to date, one that has been implemented in the GIZA (Al-Onaizan et al., 1999) and GIZA++ (Och and Ney 2003) software and adopted by nearly every SMT project. In this article, we investigate whether this algorithm makes search errors when it computes Viterbi alignments, that is, whether it returns alignments that are sub-optimal according to a trained model.

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Kuchaiev, Oleksii, Tijana Milenković, Vesna Memišević, Wayne Hayes, and Nataša Pržulj. "Topological network alignment uncovers biological function and phylogeny." Journal of The Royal Society Interface 7, no. 50 (2010): 1341–54. http://dx.doi.org/10.1098/rsif.2010.0063.

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Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology and disease. Comparison and alignment of biological networks will probably have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological

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Lin, F., Q. Chen, and L. M. Peng. "REW– exit-wave reconstruction and alignments for focus-variation high-resolution transmission electron microscopy images." Journal of Applied Crystallography 40, no. 3 (2007): 614. http://dx.doi.org/10.1107/s0021889807008588.

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A Windows-based computer program has been developed for exit-wave reconstruction and experimental high-resolution transmission electron microscopy image alignment. While the exit-wave reconstruction is performed mainly using the maximum-likelihood method, image alignments may be carried out using several algorithms, including the time-consuming but robust genetic algorithm.

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Lin, Weiwei, and Reiko Haga. "Matching Cyber Security Ontologies through Genetic Algorithm-Based Ontology Alignment Technique." Security and Communication Networks 2021 (November 30, 2021): 1–7. http://dx.doi.org/10.1155/2021/4856265.

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Security ontology can be used to build a shared knowledge model for an application domain to overcome the data heterogeneity issue, but it suffers from its own heterogeneity issue. Finding identical entities in two ontologies, i.e., ontology alignment, is a solution. It is important to select an effective similarity measure (SM) to distinguish heterogeneous entities. However, due to the complex semantic relationships among concepts, no SM is ensured to be effective in all alignment tasks. The aggregation of SMs so that their advantages and disadvantages complement each other directly affects t

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Antunes, Cauã Roca, Alexandre Rademaker, and Mara Abel. "A faster and less aggressive algorithm for correcting conservativity violations in ontology alignments." Applied Ontology 16, no. 3 (2021): 277–96. http://dx.doi.org/10.3233/ao-210243.

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Ontologies are computational artifacts that model consensual aspects of reality. In distributed contexts, applications often need to utilize information from several distinct ontologies. In order to integrate multiple ontologies, entities modeled in each ontology must be matched through an ontology alignment. However, imperfect alignments may introduce inconsistencies. One kind of inconsistency, which is often introduced, is the violation of the conservativity principle, that states that the alignment should not introduce new subsumption relations between entities from the same source ontology

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Ji, Yukai, Tao Huang, Chunlai Ma, Chao Hu, Zhanfeng Wang, and Anmin Fu. "IMCSA: Providing Better Sequence Alignment Space for Industrial Control Protocol Reverse Engineering." Security and Communication Networks 2022 (November 24, 2022): 1–9. http://dx.doi.org/10.1155/2022/8026280.

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Nowadays, with the wide application of industrial control facilities, industrial control protocol reverse engineering has significant security implications. The reverse method of industrial protocol based on sequence alignment is the current mainstream method because of its high accuracy. However, this method will incur a huge time overhead due to unnecessary alignments during the sequence alignment process. In this paper, we optimize the traditional sequence alignment method by combining the characteristics of industrial control protocols. We improve the frequent sequence mining algorithm, Ap

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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.

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Sequence alignment algorithms are fundamental to modern bioinformatics. Sequence alignments are widely used in diverse applications such as phylogenetic analysis, database searches for related sequences to aid identification of unknown protein domain structures and classification of proteins and protein domains. Additionally, alignment algorithms are integral to the location of related proteins to secure understanding of unknown protein functions, to suggest the folded structure of proteins of unknown structure from location of homologous proteins and/or by locating homologous domains of known

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Cavanaugh, 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.

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Sequence alignment algorithms are fundamental to modern bioinformatics. Sequence alignments are widely used in diverse applications such as phylogenetic analysis, database searches for related sequences to aid identification of unknown protein domain structures and classification of proteins and protein domains. Additionally, alignment algorithms are integral to the location of related proteins to secure understanding of unknown protein functions, to suggest the folded structure of proteins of unknown structure from location of homologous proteins and/or by locating homologous domains of known

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Chen, Jing, and Jia Huang. "A novel network aligner for the analysis of multiple protein-protein interaction networks." Computer Science and Information Systems, no. 00 (2021): 30. http://dx.doi.org/10.2298/csis200909030c.

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The analysis of protein-protein interaction networks can transfer the knowledge of well-studied biological functions to functions that are not yet adequately investigated by constructing networks and extracting similar network structures in different species. Multiple network alignment can be used to find similar regions among multiple networks. In this paper, we introduce Accurate Combined Clustering Multiple Network Alignment (ACCMNA), which is a new and accurate multiple network alignment algorithm. It uses both topology and sequence similarity information. First, the importance of all the

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Tang, Jun, Hongwei Bian, Heng Ma, and Rongying Wang. "One-Step Initial Alignment Algorithm for SINS in the ECI Frame Based on the Inertial Attitude Measurement of the CNS." Sensors 22, no. 14 (2022): 5123. http://dx.doi.org/10.3390/s22145123.

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To solve the problem of high-precision and fast initial alignment for the Strapdown Inertial Navigation System (SINS) under both dynamic and static conditions, the high-precision attitude measured by the celestial navigation system (CNS) is used as the reference information for the initial alignment. The alignment algorithm is derived in the Earth-centered inertial (ECI) frame. Compared with the alignment algorithm in the navigation frame, it is independent of position parameters and avoids the influence of the approximate error caused by the dynamic deflection angle. In addition, hull deforma

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Chauve, Cedric, Julien Courtiel, and Yann Ponty. "Counting, Generating, Analyzing and Sampling Tree Alignments." International Journal of Foundations of Computer Science 29, no. 05 (2018): 741–67. http://dx.doi.org/10.1142/s0129054118420030.

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Pairwise ordered tree alignment are combinatorial objects that appear in important applications, such as RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninformative, and detrimental to any probabilistic analysis. In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic c

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SALEM, SAEED, MOHAMMED J. ZAKI, and CHRISTOPHER BYSTROFF. "ITERATIVE NON-SEQUENTIAL PROTEIN STRUCTURAL ALIGNMENT." Journal of Bioinformatics and Computational Biology 07, no. 03 (2009): 571–96. http://dx.doi.org/10.1142/s0219720009004205.

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Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignmen

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Liner, Christopher L., and Robert G. Clapp. "Nonlinear pairwise alignment of seismic traces." GEOPHYSICS 69, no. 6 (2004): 1552–59. http://dx.doi.org/10.1190/1.1836828.

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Seismic trace alignment is a recurring need in seismic processing and interpretation. For global alignment via static shift, there are robust tools available, including crosscorrelation. However, another kind of alignment problem arises in applications as diverse as associating synthetic seismograms to field data, harmonizing P‐ and S‐wave data, residual NMO, and final multilevel flattening of common image gathers. These cases require combinations of trace compression, extension, and shift—all of which are time variant. The difficulty is to find a mapping between the traces that is in some sen

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Milano, Marianna, Pietro Hiram Guzzi, and Mario Cannataro. "Design and Implementation of New Local Alignment Algorithm for Multilayer Networks." Entropy 24, no. 9 (2022): 1272. http://dx.doi.org/10.3390/e24091272.

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Network alignment (NA) is a popular research field that aims to develop algorithms for comparing networks. Applications of network alignment span many fields, from biology to social network analysis. NA comes in two forms: global network alignment (GNA), which aims to find a global similarity, and LNA, which aims to find local regions of similarity. Recently, there has been an increasing interest in introducing complex network models such as multilayer networks. Multilayer networks are common in many application scenarios, such as modelling of relations among people in a social network or repr

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Rautiainen, Mikko, Veli Mäkinen, and Tobias Marschall. "Bit-parallel sequence-to-graph alignment." Bioinformatics 35, no. 19 (2019): 3599–607. http://dx.doi.org/10.1093/bioinformatics/btz162.

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Abstract Motivation Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence the genetic variation present in a population. Being able to align sequencing reads to such graphs is a key step for many analyses and its applications include genome assembly, read error correction and variant calling with respect to a variation graph. Results

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Demin, A. V. "Alignment algorithm for composite mirrors." Computer Optics 41, no. 2 (2017): 291–94. http://dx.doi.org/10.18287/2412-6179-2017-41-2-291-294.

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Huang, X., and K. M. Chao. "A generalized global alignment algorithm." Bioinformatics 19, no. 2 (2003): 228–33. http://dx.doi.org/10.1093/bioinformatics/19.2.228.

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Nelson, Reed, Rosa Aghdam, and Claudia Solis-Lemus. "MiNAA: Microbiome Network Alignment Algorithm." Journal of Open Source Software 9, no. 96 (2024): 5448. http://dx.doi.org/10.21105/joss.05448.

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Tang, Chuan Yi, Chin Lung Lu, Margaret Dah-Tsyr Chang, et al. "Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment." Journal of Bioinformatics and Computational Biology 01, no. 02 (2003): 267–87. http://dx.doi.org/10.1142/s0219720003000095.

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In this paper, we design a heuristic algorithm of computing a constrained multiple sequence alignment (CMSA for short) for guaranteeing that the generated alignment satisfies the user-specified constraints that some particular residues should be aligned together. If the number of residues needed to be aligned together is a constant α, then the time-complexity of our CMSA algorithm for aligning K sequences is O(αKn4), where n is the maximum of the lengths of sequences. In addition, we have built up such a CMSA software system and made several experiments on the RNase sequences, which mainly fun

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Jeong, Sang Hwa, Gwang Ho Kim, and Kyoung Rae Cha. "A Study on Automation Program for the Characteristics Improvement of Optical Element Alignment System." Key Engineering Materials 326-328 (December 2006): 305–8. http://dx.doi.org/10.4028/www.scientific.net/kem.326-328.305.

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With the increasing demand for VBNS and VDSL, the development of the kernel parts of optical communication such as PLC(Planar Light Circuit), Coupler, and WDM elements has increased. The optical transmitter and the receiver module need precise and mechanical alignment within a few micrometers to couple the semiconductor device, optical fiber and waveguide. The alignment and the attachment technology are very important in the fabrication of an optical element. Presently, the alignment of the optical element is time consuming, and an effective alignment algorithm has not yet to be developed. In

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Kang, Li, Lingyun Ye, and Kaichen Song. "A Fast in-Motion Alignment Algorithm for DVL Aided SINS." Mathematical Problems in Engineering 2014 (2014): 1–12. http://dx.doi.org/10.1155/2014/593692.

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Doppler velocity log (DVL) aided strapdown inertial navigation system (SINS) is a common navigation method for underwater applications. Owing to the in-motion condition and the lack of the GPS, it is a challenge to align a SINS under water. This paper proposed a complete in-motion alignment solution for both attitude and position. The velocity update equation and its integral form in the body frame are studied, and the attitude coarse alignment becomes an optimization-based attitude determination problem between the body frame velocity and the integral form of gravity. The body frame velocity

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Long, 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.

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Multiple sequence alignment (MSA) is an NP-complete and important problem in bioinformatics. Currently, profile hidden Markov model (HMM) is widely used for multiple sequence alignment. In this paper, Quantum-behaved Particle Swarm Optimization with selection operation (SQPSO) is presented, which is used to train profile HMM. Furthermore, an integration algorithm based on the profile HMM and SQPSO for the MSA is constructed. The approach is examined by using multiple nucleotides and protein sequences and compared with other algorithms. The results of the comparisons show that the HMM trained w

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Jiang, Yihang, Yuankai Qi, Will Ke Wang, et al. "EventDTW: An Improved Dynamic Time Warping Algorithm for Aligning Biomedical Signals of Nonuniform Sampling Frequencies." Sensors 20, no. 9 (2020): 2700. http://dx.doi.org/10.3390/s20092700.

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The dynamic time warping (DTW) algorithm is widely used in pattern matching and sequence alignment tasks, including speech recognition and time series clustering. However, DTW algorithms perform poorly when aligning sequences of uneven sampling frequencies. This makes it difficult to apply DTW to practical problems, such as aligning signals that are recorded simultaneously by sensors with different, uneven, and dynamic sampling frequencies. As multi-modal sensing technologies become increasingly popular, it is necessary to develop methods for high quality alignment of such signals. Here we pro

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Yan, Zheping, Lu Wang, Tongda Wang, Honghan Zhang, and Zewen Yang. "Polar Transversal Initial Alignment Algorithm for UUV with a Large Misalignment Angle." Sensors 18, no. 10 (2018): 3231. http://dx.doi.org/10.3390/s18103231.

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The conventional initial alignment algorithms are invalid in the polar region. This is caused by the rapid convergence of the Earth meridians in the high-latitude areas. However, the initial alignment algorithms are important for the accurate navigation of Unmanned Underwater Vehicles. The polar transversal initial alignment algorithm is proposed to overcome this problem. In the polar transversal initial alignment algorithm, the transversal geographic frame is chosen as the navigation frame. The polar region in the conventional frames is equivalent to the equatorial region in the transversal f

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Lebsir, Rabah, Abdesslem Layeb, and Tahi Fariza. "A Greedy Clustering Algorithm for Multiple Sequence Alignment." International Journal of Cognitive Informatics and Natural Intelligence 15, no. 4 (2021): 1–17. http://dx.doi.org/10.4018/ijcini.20211001.oa41.

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This paper presents a strategy to tackle the Multiple Sequence Alignment (MSA) problem, which is one of the most important tasks in the biological sequence analysis. Its role is to align the sequences in their entirety to derive relationships and common characteristics between a set of protein or nucleotide sequences. The MSA problem was proved to be an NP-Hard problem. The proposed strategy incorporates a new idea based on the well-known divide and conquer paradigm. This paper presents a novel method of clustering sequences as a preliminary step to improve the final alignment; this decomposit

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Wilburn, 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.

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Most methods for biological sequence homology search and alignment work with primary sequence alone, neglecting higher-order correlations. Recently, statistical physics models called Potts models have been used to infer all-by-all pairwise correlations between sites in deep multiple sequence alignments, and these pairwise couplings have improved 3D structure predictions. Here we extend the use of Potts models from structure prediction to sequence alignment and homology search by developing what we call a hidden Potts model (HPM) that merges a Potts emission process to a generative probability

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AY, FERHAT, TAMER KAHVECI, and VALÉRIE DE CRÉCY-LAGARD. "A FAST AND ACCURATE ALGORITHM FOR COMPARATIVE ANALYSIS OF METABOLIC PATHWAYS." Journal of Bioinformatics and Computational Biology 07, no. 03 (2009): 389–428. http://dx.doi.org/10.1142/s0219720009004163.

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Pathways show how different biochemical entities interact with one another to perform vital functions for the survival of an organism. Comparative analysis of pathways is crucial in identifying functional similarities that are difficult to identify by comparing individual entities that build up these pathways. When interacting entities are of single type, the problem of identifying similarities by aligning the pathways can be reduced to graph isomorphism problem. For pathways with varying types of entities such as metabolic pathways, alignment problem is even more challenging. In order to simp

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Xue, Xingsi, and Jianhua Liu. "Optimizing Ontology Alignment Through Compact MOEA/D." International Journal of Pattern Recognition and Artificial Intelligence 31, no. 04 (2017): 1759004. http://dx.doi.org/10.1142/s0218001417590042.

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In order to support semantic inter-operability in many domains through disparate ontologies, we need to identify correspondences between the entities across different ontologies, which is commonly known as ontology matching. One of the challenges in ontology matching domain is how to select weights and thresholds in the ontology aligning process to aggregate the various similarity measures to obtain a satisfactory alignment, so called ontology meta-matching problem. Nowadays, the most suitable methodology to address the ontology meta-matching problem is through Evolutionary Algorithm (EA), and

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NARIMANI, ZAHRA, HAMID BEIGY, and HASSAN ABOLHASSANI. "A NEW GENETIC ALGORITHM FOR MULTIPLE SEQUENCE ALIGNMENT." International Journal of Computational Intelligence and Applications 11, no. 04 (2012): 1250023. http://dx.doi.org/10.1142/s146902681250023x.

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Multiple sequence alignment (MSA) is one of the basic and important problems in molecular biology. MSA can be used for different purposes including finding the conserved motifs and structurally important regions in protein sequences and determine evolutionary distance between sequences. Aligning several sequences cannot be done in polynomial time and therefore heuristic methods such as genetic algorithms can be used to find approximate solutions of MSA problems. Several algorithms based on genetic algorithms have been developed for this problem in recent years. Most of these algorithms use ver

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Lee, Seyoung, Jiye Lee, and Jehee Lee. "Learning Virtual Chimeras by Dynamic Motion Reassembly." ACM Transactions on Graphics 41, no. 6 (2022): 1–13. http://dx.doi.org/10.1145/3550454.3555489.

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The Chimera is a mythological hybrid creature composed of different animal parts. The chimera's movements are highly dependent on the spatial and temporal alignments of its composing parts. In this paper, we present a novel algorithm that creates and animates chimeras by dynamically reassembling source characters and their movements. Our algorithm exploits a two-network architecture: part assembler and dynamic controller. The part assembler is a supervised learning layer that searches for the spatial alignment among body parts, assuming that the temporal alignment is provided. The dynamic cont

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Och, Franz Josef, and Hermann Ney. "A Systematic Comparison of Various Statistical Alignment Models." Computational Linguistics 29, no. 1 (2003): 19–51. http://dx.doi.org/10.1162/089120103321337421.

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We present and compare various methods for computing word alignments using statistical or heuristic models. We consider the five alignment models presented in Brown, Della Pietra, Della Pietra, and Mercer (1993), the hidden Markov alignment model, smoothing techniques, and refinements. These statistical models are compared with two heuristic models based on the Dice coefficient. We present different methods for combining word alignments to perform a symmetrization of directed statistical alignment models. As evaluation criterion, we use the quality of the resulting Viterbi alignment compared t

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Kamionskaya, A. M., and M. A. Korotkova. "Multiple Alignment of Promoter Sequences from the Human Genome." Biotekhnologiya 36, no. 4 (2020): 7–14. http://dx.doi.org/10.21519/0234-2758-2020-36-4-7-14.

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A new algorithm for multiple alignment of nucleotide sequences of MAHDS has been developed. A statistically significant multiple alignment of promoter sequences from the human genome was first created using this algorithm. Based on the constructed alignments, 25 classes of promoter sequences were created with the volume of each class exceeding 100 sequences. The classes of promoters can be used to search for promoter sequences in eukaryotic genomes. promoter, class, dynamic programming, human genome. The work was partially supported by the Russian Foundation for Basic Research (Grant no. 20-01

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Xue, Xingsi, Xiaojing Wu, and Junfeng Chen. "Optimizing Ontology Alignment Through an Interactive Compact Genetic Algorithm." ACM Transactions on Management Information Systems 12, no. 2 (2021): 1–17. http://dx.doi.org/10.1145/3439772.

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Ontology provides a shared vocabulary of a domain by formally representing the meaning of its concepts, the properties they possess, and the relations among them, which is the state-of-the-art knowledge modeling technique. However, the ontologies in the same domain could differ in conceptual modeling and granularity level, which yields the ontology heterogeneity problem. To enable data and knowledge transfer, share, and reuse between two intelligent systems, it is important to bridge the semantic gap between the ontologies through the ontology matching technique. To optimize the ontology align

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FUTAMURA, NATSUHIKO, SRINIVAS ALURU, and XIAOQIU HUANG. "PARALLEL SYNTENIC ALIGNMENTS." Parallel Processing Letters 13, no. 04 (2003): 689–703. http://dx.doi.org/10.1142/s0129626403001604.

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Given two genomic DNA sequences, the syntenic alignment problem is to compute an ordered list of subsequences for each sequence such that the corresponding subsequence pairs exhibit a high degree of similarity. Syntenic alignments are useful in comparing genomic DNA from related species and in identifying conserved genes. In this paper, we present a parallel algorithm for computing syntenic alignments that runs in [Formula: see text] time, where m and n are the respective lengths of the two genomic sequences, and p is the number of processors used. Our algorithm is time optimal with respect to

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Shegay, Maksim V., Vytas K. Švedas, Vladimir V. Voevodin, Dmitry A. Suplatov, and Nina N. Popova. "Guide tree optimization with genetic algorithm to improve multiple protein 3D-structure alignment." Bioinformatics 38, no. 4 (2021): 985–89. http://dx.doi.org/10.1093/bioinformatics/btab798.

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Abstract Motivation With the increasing availability of 3D-data, the focus of comparative bioinformatic analysis is shifting from protein sequence alignments toward more content-rich 3D-alignments. This raises the need for new ways to improve the accuracy of 3D-superimposition. Results We proposed guide tree optimization with genetic algorithm (GA) as a universal tool to improve the alignment quality of multiple protein 3D-structures systematically. As a proof of concept, we implemented the suggested GA-based approach in popular Matt and Caretta multiple protein 3D-structure alignment (M3DSA)

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Huang, Yikun, Xingsi Xue, and Chao Jiang. "Optimizing Ontology Alignment through Improved NSGA-II." Discrete Dynamics in Nature and Society 2020 (June 19, 2020): 1–8. http://dx.doi.org/10.1155/2020/8586058.

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Over the past decades, a large number of complex optimization problems have been widely addressed through multiobjective evolutionary algorithms (MOEAs), and the knee solutions of the Pareto front (PF) are most likely to be fitting for the decision maker (DM) without any user preferences. This work investigates the ontology matching problem, which is a challenge in the semantic web (SW) domain. Due to the complex heterogeneity between two different ontologies, it is arduous to get an excellent alignment that meets all DMs’ demands. To this end, a popular MOEA, i.e., nondominated sorting geneti

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Naznin, Farhana, Ruhul Sarker, and Daryl Essam. "Progressive Alignment Method Using Genetic Algorithm for Multiple Sequence Alignment." IEEE Transactions on Evolutionary Computation 16, no. 5 (2012): 615–31. http://dx.doi.org/10.1109/tevc.2011.2162849.

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Ji, Guo Li, Long Teng Chen, and Liang Liang Chen. "Two-Level Parallel Alignment Based on Sequence Parallel Vectorization." Applied Mechanics and Materials 490-491 (January 2014): 757–62. http://dx.doi.org/10.4028/www.scientific.net/amm.490-491.757.

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This paper proposed a way of two-level parallel alignment based on sequence parallel vectorization with GPU acceleration on the Fermi architecture, which integrates sequence parallel vectorization, parallel k-means clustering approximate alignment and parallel Smith-Waterman algorithm. The method converts sequence alignment into vector alignment by first. Then it uses k-means alignment to divide sequences into several groups and reduce the size of sequence data. The expected accurate alignment result is achieved using parallel Smith-Waterman algorithm. The high-throughput mouse T-cell receptor

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Schroedl, 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.

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Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to push the limits of exact algorithms further. Since MSA can be cast as a classical path finding problem, it is attracting a growing number of AI researchers interested in heuristic search algorithms as a challenge with actual practical relevance. In this paper, we first review two previous, complementary lines of research. Based on Hirschberg's algorithm, Dynami

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Kim, Hyungjong. "Wafer Center Alignment System of Transfer Robot Based on Reduced Number of Sensors." Sensors 22, no. 21 (2022): 8521. http://dx.doi.org/10.3390/s22218521.

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This brief presents a wafer alignment algorithm with reduced sensor number that obtains the relative distance of the wafer center and the robot hand. By ‘reduced number’, in spite of smaller number of sensors than the conventional method, we mean an improved method which achieves the similar results to pre-existing algorithms. Indeed, it can be designed with only three sensor data, less than four sensors of the conventional algorithm. Thus, some advantages of the proposed alignment algorithm include that it can be designed with low cost and less computing power. The proposed alignment algorith

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ABOUELHODA, MOHAMED I., ROBERT GIEGERICH, BEHSHAD BEHZADI, and JEAN-MARC STEYAERT. "ALIGNMENT OF MINISATELLITE MAPS BASED ON RUN-LENGTH ENCODING SCHEME." Journal of Bioinformatics and Computational Biology 07, no. 02 (2009): 287–308. http://dx.doi.org/10.1142/s0219720009004060.

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Subsequent duplication events are responsible for the evolution of the minisatellite maps. Alignment of two minisatellite maps should therefore take these duplication events into account, in addition to the well-known edit operations. All algorithms for computing an optimal alignment of two maps, including the one presented here, first deduce the costs of optimal duplication scenarios for all substrings of the given maps. Then, they incorporate the pre-computed costs in the alignment recurrence. However, all previous algorithms addressing this problem are dependent on the number of distinct ma

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PATEL, 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.

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We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process,

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Li, Hanzhou, Quan Pan, Xiaoxu Wang, Xiangjun Jiang, and Lin Deng. "Kalman Filter Design for Initial Precision Alignment of a Strapdown Inertial Navigation System on a Rocking Base." Journal of Navigation 68, no. 1 (2014): 184–95. http://dx.doi.org/10.1017/s0373463314000575.

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In this paper, a conventional Strapdown Inertial Navigation System (SINS) alignment method on a disturbed base is analysed. A novel method with an attitude tracking idea is proposed for the rocking base alignment. It is considered in this method that the alignment algorithm should track the rocking base attitude real changes in the alignment process, but not excessively restrain disturbance. According to this idea, a rapid alignment algorithm is devised for the rocking base. In the algorithm, coarse alignment is carried out within 30 s in the inertial frame with alignment precision less than 2

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