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Relevant bibliographies by topics / Alignment algorithm

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Journal articles

Academic literature on the topic 'Alignment algorithm'

Author: Grafiati

Published: 25 May 2024

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Journal articles on the topic "Alignment algorithm"

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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2

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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3

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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5

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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6

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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7

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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8

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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9

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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10

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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