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作者： Ratsoma, M. S. North-West University

学位级别：硕士

South Africa introduced smart ID cards in 2013 for identification and authentication of South African citizens. This came as an improvement on the old green bar-coded ID book in which authentication was not secure enough. However, the use of the smart-card for authentication comes with new problems. The minutia points that are stored in the smart-card, due to standardisation, appear to cause accuracy problems when used with on-card minutiae comparison algorithms. This study set out to investigate how the compact-card and record formats of minutia points affect the comparison accuracy and to also find out an algorithm that performs better with the minutiae format developed for use in smart-cards. This was followed by identification of a problem which had not been studied in depth before, pertaining to the formats of minutia points used for on-card comparison. The methodology of the study is presented and algorithm designs are presented. An analysis of variance is also shown for the analysis of minutia points, and in doing so it was revealed that the minutia points are not significantly different from one another; although differences exist. This led to a detailed study of the MOC algorithms, where two algorithms were selected due to their basic structure that separated the algorithms. The two categories of matching algorithms used are the local-features and the global-features based algorithms. The nearest-neighbourhood algorithm and the alignment algorithm fall into these categories respectively. These matching algorithms were implemented and also verified to ensure that they are within their specifications. In addition to implementing matching algorithms, the minutia points were also encoded in the 3-byte and 5-byte formats. The results showed that the template does affect the accuracy and the effect is not the same on each of the algorithms. However, through manipulation of the resolutions that cause some loss of accuracy, the algorithms' performance with 3-byte c

关键词： Match-on-Card alignment algorithm nearest-neighbourhood algorithm accuracy resolution ISO/IEC 19794-2:2011 compact card format

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High precision optical fiber alignment using tube laser bending

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INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY 2016年第1-4期86卷 953-961页

作者： Folkersma, K. G. P. Romer, G. R. B. E. Brouwer, D. M. Herder, J. L. Univ Twente Fac Engn Technol Chair Appl Laser Technol Drienerlolaan 5 NL-7522 NB Enschede Netherlands

In this paper, we present a method to align optical fibers within 0.2 mu m of the optimal position, using tube laser bending and in situ measuring of the coupling efficiency. For near-UV wavelengths, passive alignment of the fibers with respect to the waveguides on photonic integrated circuit chips does not suffice. In prior research, it was shown that permanent position adjustments to an optical fiber by tube laser bending meets the accuracy requirements for this application. This iterative alignment can be done after any assembly steps. A method was developed previously that selects the optimal laser power and laser spot position on the tube, to minimize the number of iterations required to reach the target position. In this paper, that method is extended to the case where the absolute position of the fiber tip cannot be measured. By exploiting the thermal expansion motion at a relatively low laser power, the fiber tip can be moved without permanent deformation (only elastic strain) of the tube. An algorithm has been developed to search for the optimal fiber position, by actively measuring and maximizing the coupling efficiency. This search is performed before each bending step. Experiments have shown that it is possible to align the fiber with an accuracy of 0.2 mu m using this approach.

关键词： Fiber alignment Laser tube forming Laser adjustment algorithms alignment algorithm

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Easy and Fast Reconstruction of a 3D Avatar with an RGB-D Sensor

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SENSORS 2017年第5期17卷 1113-1113页

作者： Mao, Aihua Zhang, Hong Liu, Yuxin Zheng, Yinglong Li, Guiqing Han, Guoqiang South China Univ Technol Sch Comp Sci & Engn Guangzhou 510006 Guangdong Peoples R China

This paper proposes a new easy and fast 3D avatar reconstruction method using an RGB-D sensor. Users can easily implement human body scanning and modeling just with a personal computer and a single RGB-D sensor such as a Microsoft Kinect within a small workspace in their home or office. To make the reconstruction of 3D avatars easy and fast, a new data capture strategy is proposed for efficient human body scanning, which captures only 18 frames from six views with a close scanning distance to fully cover the body;meanwhile, efficient alignment algorithms are presented to locally align the data frames in the single view and then globally align them in multi-views based on pairwise correspondence. In this method, we do not adopt shape priors or subdivision tools to synthesize the model, which helps to reduce modeling complexity. Experimental results indicate that this method can obtain accurate reconstructed 3D avatar models, and the running performance is faster than that of similar work. This research offers a useful tool for the manufacturers to quickly and economically create 3D avatars for products design, entertainment and online shopping.

关键词： human body 3D reconstruction RBG-D sensor scanning strategy alignment algorithm

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AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments

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BMC BIOINFORMATICS 2016年第1期17卷 1-6页

作者： Shafee, Thomas Cooke, Ira La Trobe Univ La Trobe Inst Mol Sci Dept Biochem & Genet Melbourne Vic 3086 Australia James Cook Univ Dept Mol & Cell Biol Townsville Qld 4811 Australia

Background: Alternative sequence alignment algorithms yield different results. It is therefore useful to quantify the similarities and differences between alternative alignments of the same sequences. These measurements can identify regions of consensus that are likely to be most informative in downstream analysis. They can also highlight systematic differences between alignments that relate to differences in the alignment algorithms themselves. Results: Here we present a simple method for aligning two alternative multiple sequence alignments to one another and assessing their similarity. Differences are categorised into merges, splits or shifts in one alignment relative to the other. A set of graphical visualisations allow for intuitive interpretation of the data. Conclusions: AlignStat enables the easy one-off online use of MSA similarity comparisons or into R pipelines.

关键词： Similarity Score alignment algorithm Equivalency Function Dissimilarity Matrix Reference alignment

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Is Sequence alignment an Art or a Science?

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SYSTEMATIC BOTANY 2015年第1期40卷 14-26页

作者： Morrison, David A. Uppsala Univ Syst Biol S-75236 Uppsala Sweden

Aligning multiple nucleotide sequences is a prerequisite for many if not most comparative sequence analyses in evolutionary biology. These alignments are often recognized as representing the homology relations of the aligned nucleotides, but this is a necessary requirement only for phylogenetic analyses. Unfortunately, existing computer programs for sequence alignment are not based explicitly on detecting the homology of nucleotides, and so there is a notable gap in the existing bioinformatics repertoire. If homology is the goal, then current alignment procedures may be more art than science. To resolve this issue, I present a simple conceptual scheme relating the traditional criteria for homology to the features of nucleotide sequences. These relations can then be used as optimization criteria for nucleotide sequence alignments. I point out the way in which current computer programs for multiple sequence alignment relate to these criteria, noting that each of them usually implements only one criterion. This explains the apparent dissatisfaction with computerized sequence alignment in phylogenetics, as any program that truly tried to produce alignments based on homology would need to simultaneously optimize all of the criteria.

关键词： Multiple alignment alignment algorithm sequence homology

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An analytical workflow for accurate variant discovery in highly divergent regions

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BMC GENOMICS 2016年第1期17卷 703-703页

作者： Tian, Shulan Yan, Huihuang Neuhauser, Claudia Slager, Susan L. Mayo Clin Dept Hlth Sci Res Div Biomed Stat & Informat 200 1st St SW Rochester MN 55905 USA Univ Minnesota Inst Informat Minneapolis MN 55455 USA

Background: Current variant discovery methods often start with the mapping of short reads to a reference genome;yet, their performance deteriorates in genomic regions where the reads are highly divergent from the reference sequence. This is particularly problematic for the human leukocyte antigen (HLA) region on chromosome 6p21.3. This region is associated with over 100 diseases, but variant calling is hindered by the extreme divergence across different haplotypes. Results: We simulated reads from chromosome 6 exonic regions over a wide range of sequence divergence and coverage depth. We systematically assessed combinations between five mappers and five callers for their performance on simulated data and exome-seq data from NA12878, a well-studied individual in which multiple public call sets have been generated. Among those combinations, the number of known SNPs differed by about 5 % in the non-HLA regions of chromosome 6 but over 20 % in the HLA region. Notably, GSNAP mapping combined with GATK UnifiedGenotyper calling identified about 20 % more known SNPs than most existing methods without a noticeable loss of specificity, with 100 % sensitivity in three highly polymorphic HLA genes examined. Much larger differences were observed among these combinations in INDEL calling from both non-HLA and HLA regions. We obtained similar results with our internal exome-seq data from a cohort of chronic lymphocytic leukemia patients. Conclusions: We have established a workflow enabling variant detection, with high sensitivity and specificity, over the full spectrum of divergence seen in the human genome. Comparing to public call sets from NA12878 has highlighted the overall superiority of GATK UnifiedGenotyper, followed by GATK HaplotypeCaller and SAMtools, in SNP calling, and of GATK HaplotypeCaller and Platypus in INDEL calling, particularly in regions of high sequence divergence such as the HLA region. GSNAP and Novoalign are the ideal mappers in combination with the above

关键词： alignment algorithm Chronic lymphocytic leukemia Exome sequencing Human leukocyte antigen Variant calling

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Identification of Glycopeptides with Multiple Hydroxylysine O-Glycosylation Sites by Tandem Mass Spectrometry

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JOURNAL OF PROTEOME RESEARCH 2015年第12期14卷 5099-5108页

作者： Zhang, Yanlin Yu, Chuan-Yih Song, Ehwang Li, Shuai Cheng Mechref, Yehia Tang, Haixu Liu, Xiaowen City Univ Hong Kong Dept Comp Sci Kowloon Hong Kong Peoples R China Indiana Univ Sch Informat & Comp Bloomington IN 47405 USA Texas Tech Univ Dept Chem & Biochem Lubbock TX 79409 USA Indiana Univ Purdue Univ Dept BioHlth Informat Indianapolis IN 46202 USA Indiana Univ Sch Med Ctr Computat Biol & Bioinformat Indianapolis IN 46202 USA

Glycosylation is one of the most common post-translational modifications in proteins, existing in similar to 50% of mammalian proteins. Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification;however, this problem is still challenging because of the enormous diversity of glycan structures and the microheterogeneity of glycans. In addition, a glycopeptide may contain multiple glycosylation sites, making the problem complex. Current software tools often fail to identify glycopeptides with multiple glycosylation sites, and hence we present GlycoMID, a graph-based spectral alignment algorithm that can identify glycopeptides with multiple hydroxylysine O-glycosylation sites by tandem mass spectra. GlycoMID was tested on mass spectrometry data sets of the bovine collagen alpha-(II) chain protein, and experimental results showed that it identified more glycopeptide-spectrum matches than other existing tools, including many glycopeptides with two glycosylation sites.

关键词： alignment algorithm O-linked glycosylation glycopeptide identification collagen alpha-(II) chain MS/MS spectra

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Efficient protein alignment algorithm for protein search

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BMC BIOINFORMATICS 2010年第Sup1期11卷 S34-S34页

作者： Lu, Zaixin Zhao, Zhiyu Fu, Bin Univ Texas Pan Amer Dept Comp Sci Edinburg TX 78539 USA Univ New Orleans Dept Comp Sci New Orleans LA 70148 USA

Background: Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups;therefore protein structure alignment algorithms are very helpful for protein biologists. However, an accurate alignment algorithm itself may be insufficient for effective discovering of structural relationships among tens of thousands of proteins. Due to the exponentially increasing amount of protein structural data, a fast and accurate structure alignment tool is necessary to access protein classification and protein similarity search;however, the complexity of current alignment algorithms are usually too high to make a fully alignment-based classification and search practical. Results: We have developed an efficient protein pairwise alignment algorithm and applied it to our protein search tool, which aligns a query protein structure in the pairwise manner with all protein structures in the Protein Data Bank (PDB) to output similar protein structures. The algorithm can align hundreds of pairs of protein structures in one second. Given a protein structure, the tool efficiently discovers similar structures from tens of thousands of structures stored in the PDB always in 2 minutes in a single machine and 20 seconds in our cluster of 6 machines. The algorithm has been fully implemented and is accessible online at our webserver, which is supported by a cluster of computers. Conclusion: Our algorithm can work out hundreds of pairs of protein alignments in one second. Therefore, it is very suitable for protein search. Our experimental results show that it is more accurate than other well known protein search systems in finding proteins which are structurally similar at SCOP family and superfamily levels, and its speed is also competitive with those systems. In terms of the pairwise alignment performance, it is as good as some well known alignment algorithms.

关键词： Protein Data Bank Local alignment alignment algorithm Query Protein alignment Length

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A genome alignment algorithm based on compression

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BMC BIOINFORMATICS 2010年第1期11卷 1-16页

作者： Minh Duc Cao Dix, Trevor I. Allison, Lloyd Monash Univ Clayton Sch Informat Technol Clayton Vic 3800 Australia

Background: Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of the two sequences. They are often computationally expensive and unable to deal with low information regions. Furthermore, they lack a well-principled objective function to measure the performance of sets of parameters. Since genomic sequences carry genetic information, this article proposes that the information content of each nucleotide in a position should be considered in sequence alignment. An information-theoretic approach for pairwise genome local alignment, namely XMAligner, is presented. Instead of comparing sequences at the character level, XMAligner considers a pair of nucleotides from two sequences to be related if their mutual information in context is significant. The information content of nucleotides in sequences is measured by a lossless compression technique. Results: Experiments on both simulated data and real data show that XMAligner is superior to conventional methods especially on distantly related sequences and statistically biased data. XMAligner can align sequences of eukaryote genome size with only a modest hardware requirement. Importantly, the method has an objective function which can obviate the need to choose parameter values for high quality alignment. The alignment results from XMAligner can be integrated into a visualisation tool for viewing purpose. Conclusions: The information-theoretic approach for sequence alignment is shown to overcome the mentioned problems of conventional character matching alignment methods. The article shows that, as genomic sequences are meant to carry information, considering the information content of nucleotides is helpful for genomic sequence alignment. Availability: Downloadable binaries, documentation and data can be found at ftp://***/software/DNAcompress-XM/XMAligner/.

关键词： Information Content Reference Sequence Hash Table alignment algorithm alignment Score

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In-plane laser forming for high precision alignment

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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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