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In-plane laser forming for high precision alignment

OPTICAL ENGINEERING 2014年第12期53卷 126105-1-126105-12页

作者： Folkersma, Ger Romer, Gert-Willem Brouwer, Dannis In 't Veld, Bert Huis Univ Twente Fac Engn Technol Chair Appl Laser Technol NL-7522 NB Enschede Netherlands

Laser microforming is extensively used to align components with submicrometer accuracy, often after assembly. While laser-bending sheet metal is the most common laser-forming mechanism, the in-plane upsetting mechanism is preferred when a high actuator stiffness is required. A three-bridge planar actuator made out of Invar 36 sheet was used to characterize this mechanism by experiments, finite element method modeling, and a fast-reduced model. The predictions of the thermal models agree well with the temperature measurements, while the final simulated displacement after 15 pulses deviates up to a factor of 2 from the measurement, using standard isotropic hardening models. Furthermore, it was found from the experiments and models that a small bridge width and a large bridge thickness are beneficial to decrease the sensitivity to disturbances in the process. The experiments have shown a step size as small as 0.1 mu m, but with a spread of 20%. This spread is attributed to scattering in surface morphology, which affects the absorbed laser power. To decrease the spread and increase the positioning accuracy, an adapted closed-loop learning algorithm is proposed. Simulations using the reduced model showed that 78% of the alignment trials were within the required accuracy of +/- 0.1 mu m. (C) 2014 Society of Photo-Optical Instrumentation Engineers (SPIE)

关键词： laser hammering fiber alignment alignment algorithm microactuator three-bridge actuator finite element model reduced model

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alignment algorithms for planar optical waveguides

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OPTICAL ENGINEERING 2012年第10期51卷 103401-103401页

作者： Zheng, Yu Duan, Ji-an Cent S Univ State Key Lab High Performance Complex Mfg Changsha 410083 Hunan Peoples R China

Planar optical waveguides are the key elements in a modern, high-speed optical network. An important problem facing the optical fiber communication system is optical-axis alignment and coupling between waveguide chips and transmission fibers. The advantages and disadvantages of the various algorithms used for the optical-axis alignment, namely, hill-climbing, pattern search, and genetic algorithm are analyzed. A new optical-axis alignment for planar optical waveguides is presented which is a composite of a genetic algorithm and a pattern search algorithm. Experiments have proved the proposed alignment's feasibility;compared with hill climbing, the search process can reduce the number of movements by 88% and reduce the search time by 83%. Moreover, the search success rate in the experiment can reach 100%. (C) 2012 Society of Photo-Optical Instrumentation Engineers (SPIE). [DOI: 10.1117/***.51.10.103401]

关键词： planar optical waveguide aligning and coupling alignment algorithm genetic algorithm

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Efficient alignment of RNA secondary structures using sparse dynamic programming

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BMC BIOINFORMATICS 2013年第1期14卷 1-15页

作者： Zhong, Cuncong Zhang, Shaojie Univ Cent Florida Dept Elect Engn & Comp Sci Orlando FL 32816 USA

Background: Current advances of the next-generation sequencing technology have revealed a large number of un-annotated RNA transcripts. Comparative study of the RNA structurome is an important approach to assess their biological functionalities. Due to the large sizes and abundance of the RNA transcripts, an efficient and accurate RNA structure-structure alignment algorithm is in urgent need to facilitate the comparative study. Despite the importance of the RNA secondary structure alignment problem, there are no computational tools available that provide high computational efficiency and accuracy. In this case, designing and implementing such an efficient and accurate RNA secondary structure alignment algorithm is highly desirable. Results: In this work, through incorporating the sparse dynamic programming technique, we implemented an algorithm that has an O(n(3)) expected time complexity, where n is the average number of base pairs in the RNA structures. This complexity, which can be shown assuming the polymer-zeta property, is confirmed by our experiments. The resulting new RNA secondary structure alignment tool is called ERA. Benchmark results indicate that ERA can significantly speedup RNA structure-structure alignments compared to other state-of-the-art RNA alignment tools, while maintaining high alignment accuracy. Conclusions: Using the sparse dynamic programming technique, we are able to develop a new RNA secondary structure alignment tool that is both efficient and accurate. We anticipate that the new alignment algorithm ERA will significantly promote comparative RNA structure studies. The program, ERA, is freely available at http://***/ERA.

关键词： Time Complexity Structure alignment alignment algorithm alignment Score Pruning Technique

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Highly improved homopolymer aware nucleotide-protein alignments with 454 data

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BMC BIOINFORMATICS 2012年第1期13卷 1-13页

作者： Lysholm, Fredrik Linkoping Univ IFM Bioinformat & SeRC Swedish E Sci Res Ctr S-58183 Linkoping Sweden Karolinska Inst Dept Cell & Mol Biol Sci Life Lab S-17177 Stockholm Sweden

Background: Roche 454 sequencing is the leading sequencing technology for producing long read high throughput sequence data. Unlike most methods where sequencing errors translate to base uncertainties, 454 sequencing inaccuracies create nucleotide gaps. These gaps are particularly troublesome for translated search tools such as BLASTx where they introduce frame-shifts and result in regions of decreased identity and/or terminated alignments, which affect further analysis. Results: To address this issue, the Homopolymer Aware Cross alignment Tool (HAXAT) was developed. HAXAT uses a novel dynamic programming algorithm for solving the optimal local alignment between a 454 nucleotide and a protein sequence by allowing frame-shifts, guided by 454 flowpeak values. The algorithm is an efficient minimal extension of the Smith-Waterman-Gotoh algorithm that easily fits in into other tools. Experiments using HAXAT demonstrate, through the introduction of 454 specific frame-shift penalties, significantly increased accuracy of alignments spanning homopolymer sequence errors. The full effect of the new parameters introduced with this novel alignment model is explored. Experimental results evaluating homopolymer inaccuracy through alignments show a two to five-fold increase in Matthews Correlation Coefficient over previous algorithms, for 454-derived data. Conclusions: This increased accuracy provided by HAXAT does not only result in improved homologue estimations, but also provides un-interrupted reading-frames, which greatly facilitate further analysis of protein space, for example phylogenetic analysis. The alignment tool is available at http://***/454tools/haxat.

关键词： Dynamic Programming algorithm alignment algorithm Matthews Correlation Coefficient Torque Teno Virus alignment Model

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A survey of sequence alignment algorithms for next-generation sequencing

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BRIEFINGS IN BIOINFORMATICS 2010年第5期11卷 473-483页

作者： Li, Heng Homer, Nils Broad Inst Cambridge MA 02142 USA Univ Calif Los Angeles Dept Comp Sci Los Angeles CA 90024 USA Univ Calif Los Angeles Dept Human Genet Los Angeles CA 90024 USA

Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. A wide variety of alignment algorithms and software have been subsequently developed over the past two years. In this article, we will systematically review the current development of these algorithms and introduce their practical applications on different types of experimental data. We come to the conclusion that short-read alignment is no longer the bottleneck of data analyses. We also consider future development of alignment algorithms with respect to emerging long sequence reads and the prospect of cloud computing.

关键词： new sequencing technologies alignment algorithm sequence analysis

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Experimental exploration of the correlation coefficient of static speckles in Fresnel configuration

Experimental exploration of the correlation coefficient of s...

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Conference on Dimensional Optical Metrology and Inspection for Practical Applications

作者： Li, Dayan Kelly, Damien P. Sheridan, John T. Univ Coll Dublin SFI Strateg Res Cluster Solar Energy Convers UCD Commun & Optoelect Res Ctr Dublin 4 Ireland Tech Univ Ilmenau Fachgebiet Opt Design Inst Mikro & Nanotechnol Macronano D-98684 Ilmenau Germany

ISBN: (纸本)9780819487438

Quasi-monochromatic light reflected from an optically rough surface produces a complicated 3D speckle field. This speckle field is often described using a correlation function from which the 3D speckle properties can be examined. The derivation of the correlation function is based on a physical model where several critical assumptions about the input and output fields in the model are made. However, experimental works verifying this correlation function are rare and sometimes produce inconsistent results. In this paper, we examine some practical issues encountered when experimentally measuring this correlation function, including: The realization of the ensemble average between speckle fields at two point positions;and, The pixel integrating effect of the recording camera and the implications this has for the statistics of the measured speckle field. Following verification of the correlation function and examining the speckle decorrelation properties in 3D space, two practical applications are proposed, one is the aligning of the system optical axis with the camera center and the other is the measurement of the out-of-plane displacement of an object surface. Simulation and experimental results that support our analysis are presented.

关键词： speckle correlation coefficients ensemble average pixel integrating effect longitudinal decorrelation alignment algorithm out-of-plane displacement measurement

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Meta-alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization

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BMC BIOINFORMATICS 2011年第1期12卷 1-12页

作者： Roskin, Krishna M. Paten, Benedict Haussler, David Univ Calif Santa Cruz Dept Comp Sci Santa Cruz CA 95064 USA Univ Calif Santa Cruz Ctr Biomol Sci & Engn Santa Cruz CA 95064 USA Univ Calif Santa Cruz Howard Hughes Med Inst Santa Cruz CA 95064 USA

Background: Continuing research into the global multiple sequence alignment problem has resulted in more sophisticated and principled alignment methods. Unfortunately these new algorithms often require large amounts of time and memory to run, making it nearly impossible to run these algorithms on large datasets. As a solution, we present two general methods, Crumble and Prune, for breaking a phylogenetic alignment problem into smaller, more tractable sub-problems. We call Crumble and Prune meta-alignment methods because they use existing alignment algorithms and can be used with many current alignment programs. Crumble breaks long alignment problems into shorter sub-problems. Prune divides the phylogenetic tree into a collection of smaller trees to reduce the number of sequences in each alignment problem. These methods are orthogonal: they can be applied together to provide better scaling in terms of sequence length and in sequence depth. Both methods partition the problem such that many of the sub-problems can be solved independently. The results are then combined to form a solution to the full alignment problem. Results: Crumble and Prune each provide a significant performance improvement with little loss of accuracy. In some cases, a gain in accuracy was observed. Crumble and Prune were tested on real and simulated data. Furthermore, we have implemented a system called Job-tree that allows hierarchical sub-problems to be solved in parallel on a compute cluster, significantly shortening the run-time. Conclusions: These methods enabled us to solve gigabase alignment problems. These methods could enable a new generation of biologically realistic alignment algorithms to be applied to real world, large scale alignment problems.

关键词： alignment algorithm alignment Accuracy alignment Problem Sparse Constraint Agreement Score

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Analysis of an alignment algorithm for nonlinear dimensionality reduction

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BIT NUMERICAL MATHEMATICS 2007年第4期47卷 873-885页

作者： Ye, Qiang Zha, Hongyuan Li, Ren-Cang Univ Kentucky Dept Math Lexington KY 40506 USA Georgia Inst Technol Coll Comp Computat Sci & Engn Div Atlanta GA 30332 USA Univ Texas Arlington Dept Math Arlington TX 76019 USA

The goal of dimensionality reduction or manifold learning for a given set of high-dimensional data points, is to find a low-dimensional parametrization for them. Usually it is easy to carry out this parametrization process within a small region to produce a collection of local coordinate systems. alignment is the process to stitch those local systems together to produce a global coordinate system and is done through the computation of a partial eigendecomposition of a so-called alignment matrix. In this paper, we present an analysis of the alignment process, giving conditions under which the null space of the alignment matrix recovers the global coordinate system up to an affine transformation. We also propose a post-processing step that can determine the global coordinate system up to a rigid motion. This in turn shows that Local Tangent Space alignment method (LTSA) can recover a locally isometric embedding up to a rigid motion.

关键词： dimensionality reduction manifold learning alignment algorithm

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High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH

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BMC BIOINFORMATICS 2010年第1期11卷 1-14页

作者： Teichert, Florian Minning, Jonas Bastolla, Ugo Porto, Markus UAM CSIC Ctr Biol Mol Severo Ochoa Madrid 28049 Spain Tech Univ Darmstadt Inst Festkorperphys D-64289 Darmstadt Germany Univ Cologne Inst Theoret Phys D-50937 Cologne Germany

Background: Protein alignments are an essential tool for many bioinformatics analyses. While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence similarity gets indistinguishable from random. For such distant pairs, structure alignment is of much better quality. Nevertheless, sequence alignment is the only choice in the majority of cases where structural data is not available. This situation demands development of methods that extend the applicability of accurate sequence alignment to distantly related proteins. Results: We develop a sequence alignment method that combines the prediction of a structural profile based on the protein's sequence with the alignment of that profile using our recently published alignment tool SABERTOOTH. In particular, we predict the contact vector of protein structures using an artificial neural network based on position-specific scoring matrices generated by PSI-BLAST and align these predicted contact vectors. The resulting sequence alignments are assessed using two different tests: First, we assess the alignment quality by measuring the derived structural similarity for cases in which structures are available. In a second test, we quantify the ability of the significance score of the alignments to recognize structural and evolutionary relationships. As a benchmark we use a representative set of the SCOP (structural classification of proteins) database, with similarities ranging from closely related proteins at SCOP family level, to very distantly related proteins at SCOP fold level. Comparing these results with some prominent sequence alignment tools, we find that SABERTOOTH produces sequence alignments of better quality than those of Clustal W, T-Coffee, MUSCLE, and PSI-BLAST. HHpred, one of the most sophisticated and computationally expensive tools available, outperforms our alignment algorithm at family and superfamily levels,

关键词： Structure alignment alignment algorithm Significance Score alignment Quality Structural Profile

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Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)

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BMC BIOINFORMATICS 2010年第Sup1期11卷 S29-S29页

作者： Agarwal, Sumeet Vaz, Candida Bhattacharya, Alok Srinivasan, Ashwin Univ Oxford Comp Lab Oxford OX1 3QD England Univ Oxford Syst Biol Doctoral Training Ctr Clarendon Lab Oxford OX1 3PU England Univ Oxford Dept Phys Clarendon Lab Oxford OX1 3PU England Jawaharlal Nehru Univ Sch Informat Technol Ctr Computat Biol & Bioinformat New Delhi 110067 India Jawaharlal Nehru Univ Sch Life Sci New Delhi 110067 India Vasant Kunj Inst Area Phase II IBM India Res Lab New Delhi 110070 India Univ New S Wales Sch Engn & Comp Sci Sydney NSW Australia Univ New S Wales Ctr Hlth Informat Sydney NSW Australia

Background: It has been apparent in the last few years that small non coding RNAs (ncRNA) play a very significant role in biological regulation. Among these microRNAs (miRNAs), 22-23 nucleotide small regulatory RNAs, have been a major object of study as these have been found to be involved in some basic biological processes. So far about 706 miRNAs have been identified in humans alone. However, it is expected that there may be many more miRNAs encoded in the human genome. In this report, a "context-sensitive" Hidden Markov Model (CSHMM) to represent miRNA structures has been proposed and tested extensively. We also demonstrate how this model can be used in conjunction with filters as an ab initio method for miRNA identification. Results: The probabilities of the CSHMM model were estimated using known human miRNA sequences. A classifier for miRNAs based on the likelihood score of this "trained" CSHMM was evaluated by: (a) cross-validation estimates using known human sequences, (b) predictions on a dataset of known miRNAs, and (c) prediction on a dataset of non coding RNAs. The CSHMM is compared with two recently developed methods, miPred and CID-miRNA. The results suggest that the CSHMM performs better than these methods. In addition, the CSHMM was used in a pipeline that includes filters that check for the presence of EST matches and the presence of Drosha cutting sites. This pipeline was used to scan and identify potential miRNAs from the human chromosome 19. It was also used to identify novel miRNAs from small RNA sequences of human normal leukocytes obtained by the Deep sequencing (Solexa) methodology. A total of 49 and 308 novel miRNAs were predicted from chromosome 19 and from the small RNA sequences respectively. Conclusion: The results suggest that the CSHMM is likely to be a useful tool for miRNA discovery either for analysis of individual sequences or for genome scan. Our pipeline, consisting of a CSHMM and filters to reduce false positives shows promise as

关键词： alignment algorithm Likelihood Score miRNA Precursor miRNA Prediction miRNA Discovery

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