Статті в журналах: "Sequence analysis methods"

1

Smith, CA. "Methods in Protein Sequence Analysis." Biochemical Education 18, no. 1 (January 1990): 54–55. http://dx.doi.org/10.1016/0307-4412(90)90036-n.

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2

Seabrook, BN. "Methods in protein sequence analysis." Biochemical Education 22, no. 1 (January 1994): 59. http://dx.doi.org/10.1016/0307-4412(94)90193-7.

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3

Light, Albert. "Methods of protein sequence analysis." Analytical Biochemistry 167, no. 1 (November 1987): 210. http://dx.doi.org/10.1016/0003-2697(87)90153-9.

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4

Rybinska, Anna. "Social Sequence Analysis: Methods and Applications." Social Forces 96, no. 1 (April 4, 2017): e6-e6. http://dx.doi.org/10.1093/sf/sox026.

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5

Aisenbrey, Silke. "Social Sequence Analysis: Methods and Applications." Contemporary Sociology: A Journal of Reviews 46, no. 6 (October 27, 2017): 665–67. http://dx.doi.org/10.1177/0094306117734868i.

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6

Kuhn, Alfred. "Methods in protein sequence analysis 1986." Journal of Chromatography A 410 (January 1987): 514. http://dx.doi.org/10.1016/s0021-9673(00)90090-6.

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7

Bailey, Jerome M. "Chemical methods of protein sequence analysis." Journal of Chromatography A 705, no. 1 (June 1995): 47–65. http://dx.doi.org/10.1016/0021-9673(94)01250-i.

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8

Wilson, Clarke. "Analysis of Travel Behavior Using Sequence Alignment Methods." Transportation Research Record: Journal of the Transportation Research Board 1645, no. 1 (January 1998): 52–59. http://dx.doi.org/10.3141/1645-07.

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Sequence alignment methods are applied to daily activity data derived from the Statistics Canada 1992 General Social Survey on Time Use, with special emphasis on travel episodes and the activities that generate travel. Sequence alignment is a combinatorial procedure that gives a quantitative measure of the similarity of character sequences, which may be used to represent daily activity patterns. It accommodates all the details supplied from activity diaries including the ordering of activity episodes, their duration, and patterns of transitions from one activity to another. Analysis of daily activity patterns by using such methods offers a new way of improving understanding of travel behavior. Such an understanding is especially critical when public transport policy is being driven increasingly by budget constraints, and traffic management through congestion is considered an acceptable response to increasing travel demands. The method successfully identifies groupings of behavioral patterns, which then may be further described by using multivariate analysis of sociodemographic characteristics. A key issue in the application of the method is to determine the circumstances in which activity sequences should or should not reflect episode duration.

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9

Zeltser, Maria. "Bounded Domains of Generalized Riesz Methods with the Hahn Property." Journal of Function Spaces and Applications 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/908682.

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In 2002 Bennett et al. started the investigation to which extent sequence spaces are determined by the sequences of 0s and 1s that they contain. In this relation they defined three types of Hahn properties for sequence spaces: the Hahn property, separable Hahn property, and matrix Hahn property. In general all these three properties are pairwise distinct. If a sequence spaceEis solid and(0,1ℕ∩E)β=Eβ=ℓ1then the two last properties coincide. We will show that even on these additional assumptions the separable Hahn property and the Hahn property still do not coincide. However if we assumeEto be the bounded summability domain of a regular Riesz matrixRpor a regular nonnegative Hausdorff matrixHp, then this assumption alone guarantees thatEhas the Hahn property. For any (infinite) matrixAthe Hahn property of its bounded summability domain is related to the strongly nonatomic property of the densitydAdefined byA. We will find a simple necessary and sufficient condition for the densitydAdefined by the generalized Riesz matrixRp,mto be strongly nonatomic. This condition appears also to be sufficient for the bounded summability domain ofRp,mto have the Hahn property.

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10

Steinke, Dirk, Miguel Vences, Walter Salzburger, and Axel Meyer. "TaxI: a software tool for DNA barcoding using distance methods." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1462 (September 8, 2005): 1975–80. http://dx.doi.org/10.1098/rstb.2005.1729.

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DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than cox1 sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding.

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11

Abbott, Andrew. "Sequence Analysis: New Methods for Old Ideas." Annual Review of Sociology 21, no. 1 (August 1995): 93–113. http://dx.doi.org/10.1146/annurev.so.21.080195.000521.

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12

Beckstette, Michael, Jens T. Mailänder, Richard J. Marhöfer, Alexander Sczyrba, Enno Ohlebusch, Robert Giegerich, and Paul M. Selzer. "Genlight: Interactive high-throughput sequence analysis and comparative genomics." Journal of Integrative Bioinformatics 1, no. 1 (December 1, 2004): 90–107. http://dx.doi.org/10.1515/jib-2004-8.

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Abstract With rising numbers of fully sequenced genomes the importance of comparative genomics is constantly increasing. Although several software systems for genome comparison analyses do exist, their functionality and flexibility is still limited, compared to the manifold possible applications. Therefore, we developed Genlight(http://piranha.techfak.uni-bielefeld.de.), a Client/Server based program suite for large scale sequence analysis and comparative genomics. Genlight uses the object relational database system PostgreSQL together with a state of the art data representation and a distributed execution approach for large scale analysis tasks. The system includes a wide variety of comparison and sequence manipulation methods and supports the management of nucleotide sequences as well as protein sequences. The comparison methods are complemented by a large variety of visualization methods for the assessment of the generated results. In order to demonstrate the suitability of the system for the treatment of biological questions, Genlight was used to identify potential drug and vaccine targets of the pathogen Helicobacter pylori.

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13

Wilson, W. C. "Activity Pattern Analysis by Means of Sequence-Alignment Methods." Environment and Planning A: Economy and Space 30, no. 6 (June 1998): 1017–38. http://dx.doi.org/10.1068/a301017.

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The author describes a method of comparing sequences of characters, called sequence alignment or string matching, and illustrates its use in the analysis of daily activity patterns derived from time-use diaries. It allows definition of measures of similarity or distance between complete sequences, called global alignment, or the evaluation of the best fit of short sequences within long sequences, called local alignment. Alignments may be done pairwise to develop similarity or distance matrices that describe the relatedness of individuals in the set of sequences being examined. Pairwise alignment methods may be extended to many individuals by using multiple alignment analysis. A number of elementary hand-worked examples are provided. The basic concepts are discussed in terms of the problems of time-use research and the method is illustrated by examining diary data from a survey conducted in Reading, England. The CLUSTAL software used for the alignments was written for molecular biological research. The method offers a powerful technique for analyzing the full richness of diary data without discarding the details of episode ordering, duration, or transition. It is also possible to extend the analysis to include the context of activities, such as the presence of other persons or the location, but such extensions would require software designed for social science rather than biochemical problems. The method also offers a challenge to researchers to begin to develop theories about the determinants of daily behavior as a whole, rather than about participation in single activities or about time-budget totals.

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14

GRASSBERGER, PETER, THOMAS SCHREIBER, and CARSTEN SCHAFFRATH. "NONLINEAR TIME SEQUENCE ANALYSIS." International Journal of Bifurcation and Chaos 01, no. 03 (September 1991): 521–47. http://dx.doi.org/10.1142/s0218127491000403.

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We review several aspects of the analysis of time sequences, and concentrate on recent methods using concepts from the theory of nonlinear dynamical systems. In particular, we discuss problems in estimating attractor dimensions, entropies, and Lyapunov exponents, in reducing noise and in forecasting. For completeness and since we want to stress connections to more traditional (mostly spectrum-based) methods, we also give a short review of spectral methods.

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15

ABBOTT, ANDREW, and ANGELA TSAY. "Sequence Analysis and Optimal Matching Methods in Sociology." Sociological Methods & Research 29, no. 1 (August 2000): 3–33. http://dx.doi.org/10.1177/0049124100029001001.

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16

Maxwell, Erin E., and Luke B. Harrison. "Methods for the analysis of developmental sequence data." Evolution & Development 11, no. 1 (January 2009): 109–19. http://dx.doi.org/10.1111/j.1525-142x.2008.00307.x.

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17

Claverie, Jean-Michel, and David J. States. "Information enhancement methods for large scale sequence analysis." Computers & Chemistry 17, no. 2 (June 1993): 191–201. http://dx.doi.org/10.1016/0097-8485(93)85010-a.

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18

Petti, Samantha, and Sean R. Eddy. "Constructing benchmark test sets for biological sequence analysis using independent set algorithms." PLOS Computational Biology 18, no. 3 (March 7, 2022): e1009492. http://dx.doi.org/10.1371/journal.pcbi.1009492.

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Biological sequence families contain many sequences that are very similar to each other because they are related by evolution, so the strategy for splitting data into separate training and test sets is a nontrivial choice in benchmarking sequence analysis methods. A random split is insufficient because it will yield test sequences that are closely related or even identical to training sequences. Adapting ideas from independent set graph algorithms, we describe two new methods for splitting sequence data into dissimilar training and test sets. These algorithms input a sequence family and produce a split in which each test sequence is less than p% identical to any individual training sequence. These algorithms successfully split more families than a previous approach, enabling construction of more diverse benchmark datasets.

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19

Laufs, Stephanie, Frank A. Giordano, Agnes Hotz-Wagenblatt, Uwe Appelt, Daniel Lauterborn, Kurt Fellenberg, W. Jens Zeller, and Stefan Fruehauf. "Automated Retroviral Insertion Site Sequence Analysis and Mapping Tool Followed by Database Analysis." Blood 106, no. 11 (November 16, 2005): 5528. http://dx.doi.org/10.1182/blood.v106.11.5528.5528.

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Abstract Increasing use of retroviral vector-mediated gene transfer and recent reports on insertional mutagenesis in mice and humans created intense interest to characterize vector integrations on the genomic level. Techniques to determine insertion sites, mainly based on time consuming manual data processing and compilation, are thus commonly applied in gene therapy laboratories. Since a high variability in processing methods hampers further data comparison, there is an urgent need to systematically process the data arising from such analysis. The obtained sequences from the integration site analysis are judged to be authentic only if the matching part of the genomic query sequence is surrounded by the 5′LTR-sequence on the one side and the adapter-sequence on the other side. Therefore we developed an Integrationseq tool. In this task, different methods for converting the ABI sequence trace files to high quality sequences and for recognizing and deleting the LTR and adaptor parts of the isolated clones were implemented. If neither a primer nor a LTR could be found, the sequence is discarded. If the LTR is found on the complementary strand, the integration sequence is reversed. The remaining sequence between primer and LTR positions are taken as the n integration sequence and written to a sequence output file. We validated the Integrationseq tool using 259 trace files originating from integration site analysis (LM-PCR). Sequences can be trimmed by IntegrationSeq, leading to an increased yield of valid integration sequence detection, which has shown to be more sensitive (100%) than conventional analysis (94.3%) and 15 times faster than conventional analysis, while the specifities are equal (both 100%). Valid integration sequences get further processed with IntegrationMap for automatic genomic mapping. IntegrationMap runs 50 times faster than conventional methods and retrieves detailed information about whether integrations are located in or close to genes, the name of the gene, the exact localization in the transcriptional units and further parameters like the distance from the transcription start site to the integration. Further information, e.g. data about CpG-Islands, LINEs or SINEs, and their distances to the integration is also displayed. Output files generated by the task were found to be 99.8% identical with results retrieved by conventional mapping with the Ensembl alignment tool. Using both tools, IntegrationSeq and IntegrationMap, a validated, fast and standardized high-throughput analysis of insertion sites can be achieved for the first time.

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20

ESKIN, ELEAZAR, and SAGI SNIR. "INCORPORATING HOMOLOGUES INTO SEQUENCE EMBEDDINGS FOR PROTEIN ANALYSIS." Journal of Bioinformatics and Computational Biology 05, no. 03 (June 2007): 717–38. http://dx.doi.org/10.1142/s0219720007002734.

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Statistical and learning techniques are becoming increasingly popular for different tasks in bioinformatics. Many of the most powerful statistical and learning techniques are applicable to points in a Euclidean space but not directly applicable to discrete sequences such as protein sequences. One way to apply these techniques to protein sequences is to embed the sequences into a Euclidean space and then apply these techniques to the embedded points. In this work we introduce a biologically motivated sequence embedding, the homology kernel, which takes into account intuitions from local alignment, sequence homology, and predicted secondary structure. This embedding allows us to directly apply learning techniques to protein sequences. We apply the homology kernel in several ways. We demonstrate how the homology kernel can be used for protein family classification and outperforms state-of-the-art methods for remote homology detection. We show that the homology kernel can be used for secondary structure prediction and is competitive with popular secondary structure prediction methods. Finally, we show how the homology kernel can be used to incorporate information from homologous sequences in local sequence alignment.

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21

McBride, L. J., S. M. Koepf, R. A. Gibbs, W. Salser, P. E. Mayrand, M. W. Hunkapiller, and M. N. Kronick. "Automated DNA sequencing methods involving polymerase chain reaction." Clinical Chemistry 35, no. 11 (November 1, 1989): 2196–201. http://dx.doi.org/10.1093/clinchem/35.11.2196.

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Abstract Polymerase chain reaction (PCR) as a method for preparing DNA templates has been used for several DNA sequencing applications. An in situ procedure for directly sequencing PCR products by the dideoxy-termination method has been developed by using fluorophore-labeled sequencing primers. Completed sequence reactions were combined and loaded into a single electrophoretic lane of a fluorescence-based DNA sequence analyzer. DNA targets devoid of a universal primer sequence could be sequenced with labeled universal primers by incorporating a universal primer sequence into the PCR product. With this method, the sequence of a 351-bp region in the bacteriophage lambda genome was fully analyzed in a single lane with automatic base identification accuracy of greater than 99%. An unknown sequence, 1.7 kb long, also was sequenced by this procedure, in combination with a "PCR gene walking" strategy. Comparison of the 1110 bases in overlapping sequence data from both strands yielded only two single-base ambiguities. Automated DNA sequence analysis of the highly polymorphic HLA-DQA-1 (alpha) region in the human genome can be performed with this simple methodology. Use of this PCR-sequencing method to analyze DNA extracted from a one-month-old blood sample from an individual who is heterozygous at this locus allowed unambiguous assignment of genotype.

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22

Jung, Jong Soo. "Iterative Methods for Pseudocontractive Mappings in Banach Spaces." Abstract and Applied Analysis 2013 (2013): 1–7. http://dx.doi.org/10.1155/2013/643602.

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LetEa reflexive Banach space having a uniformly Gâteaux differentiable norm. LetCbe a nonempty closed convex subset ofE,T:C→Ca continuous pseudocontractive mapping withF(T)≠∅, andA:C→Ca continuous bounded strongly pseudocontractive mapping with a pseudocontractive constantk∈(0,1). Let{αn}and{βn}be sequences in(0,1)satisfying suitable conditions and for arbitrary initial valuex0∈C, let the sequence{xn}be generated byxn=αnAxn+βnxn-1+(1-αn-βn)Txn, n≥1.If either every weakly compact convex subset ofEhas the fixed point property for nonexpansive mappings orEis strictly convex, then{xn}converges strongly to a fixed point ofT, which solves a certain variational inequality related toA.

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23

Wang, He, Yongjian Zang, Yizhen Zhao, Dongxiao Hao, Ying Kang, Jianwen Zhang, Zichen Zhang, Lei Zhang, Zhiwei Yang, and Shengli Zhang. "Sequence Matching between Hemagglutinin and Neuraminidase through Sequence Analysis Using Machine Learning." Viruses 14, no. 3 (February 25, 2022): 469. http://dx.doi.org/10.3390/v14030469.

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To date, many experiments have revealed that the functional balance between hemagglutinin (HA) and neuraminidase (NA) plays a crucial role in viral mobility, production, and transmission. However, whether and how HA and NA maintain balance at the sequence level needs further investigation. Here, we applied principal component analysis and hierarchical clustering analysis on thousands of HA and NA sequences of A/H1N1 and A/H3N2. We discovered significant coevolution between HA and NA at the sequence level, which is closely related to the type of host species and virus epidemic years. Furthermore, we propose a sequence-to-sequence transformer model (S2STM), which mainly consists of an encoder and a decoder that adopts a multi-head attention mechanism for establishing the mapping relationship between HA and NA sequences. The training results reveal that the S2STM can effectively realize the “translation” from HA to NA or vice versa, thereby building a relationship network between them. Our work combines unsupervised and supervised machine learning methods to identify the sequence matching between HA and NA, which will advance our understanding of IAVs’ evolution and also provide a novel idea for sequence analysis methods.

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24

Ahmed, S. Ejaz. "Sequence Analysis and Related Approaches: Innovative Methods and Applications." Technometrics 62, no. 1 (January 2, 2020): 139–40. http://dx.doi.org/10.1080/00401706.2019.1708679.

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25

Felsenstein, Joe. "Computational molecular biology: Sources and methods for sequence analysis." Trends in Genetics 5 (1989): 419. http://dx.doi.org/10.1016/0168-9525(89)90203-5.

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26

WILSON, R., and L. HOOD. "High-throughput fluorescent DNA sequence analysis: Methods and automation." Methods 3, no. 1 (August 1991): 48–54. http://dx.doi.org/10.1016/s1046-2023(05)80163-x.

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27

Shukla, Rahul, and Andrzej Wiśnicki. "Iterative methods for monotone nonexpansive mappings in uniformly convex spaces." Advances in Nonlinear Analysis 10, no. 1 (January 1, 2021): 1061–70. http://dx.doi.org/10.1515/anona-2020-0170.

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Abstract We show the nonlinear ergodic theorem for monotone 1-Lipschitz mappings in uniformly convex spaces: if C is a bounded closed convex subset of an ordered uniformly convex space (X, ∣·∣, ⪯), T:C → C a monotone 1-Lipschitz mapping and x ⪯ T(x), then the sequence of averages 1 n ∑ i = 0 n − 1 T i ( x ) $ \frac{1}{n}\sum\nolimits_{i=0}^{n-1}T^{i}(x) $ converges weakly to a fixed point of T. As a consequence, it is shown that the sequence of Picard’s iteration {T n (x)} also converges weakly to a fixed point of T. The results are new even in a Hilbert space. The Krasnosel’skiĭ-Mann and the Halpern iteration schemes are studied as well.

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28

Abbas, Ali Hadi, Haider Abas AL saegh, and Furkan Sabbar ALaraji. "Sequence diversity and evolution of infectious bursal disease virus in Iraq." F1000Research 10 (April 16, 2021): 293. http://dx.doi.org/10.12688/f1000research.28421.1.

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Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2 genes were generated and sequenced. Sequences were then compared with other local and global sequences downloaded from GenBank repositories. Sequence alignment and DNA sequence analyses were achieved using MUSCLE, UGENE and MEGAx software. The molecular clock and sequence evolutionary analyses were applied using MEGAx tools. Results: The strain sequenced in this study belongs to a very virulent Infectious Bursal Disease Virus (vvIBDV) as the DNA and phylogenetic analysis of VP1 and VP2 gene sequences showed a mutual clustering with similar sequences belonging to vvIBDV genogroup 3. Analyses of the hyper variable region of VP2 gene (hvVP2) of IBDV isolates from Iraq indicates a presence of sequence diversity. Interestingly, the two vaccine strains Ventri IBDV Plus and ABIC MB71 that showed the highest sequence similarity to the local isolates in the hvVP2 region are not used in vaccination routine against IBDV in Iraq. Conclusion: Sequences of vvIBDV in Iraq are diverse. Remarkably, some of the available vaccine strains show high sequence similarity with local strains in Iraq; however, they are not included in the routine vaccination programs. Analysis of more samples involving more geographical regions is needed to draw a detailed map of antigenic diversity of IBDV in Iraq.

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Abbas, Ali Hadi, Haider Abas AL saegh, and Furkan Sabbar ALaraji. "Sequence diversity and evolution of infectious bursal disease virus in Iraq." F1000Research 10 (September 2, 2021): 293. http://dx.doi.org/10.12688/f1000research.28421.2.

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Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2 genes were generated and sequenced. Sequences were then compared with other local and global sequences downloaded from GenBank repositories. Sequence alignment and DNA sequence analyses were achieved using MUSCLE, UGENE and MEGAx software. The molecular clock and sequence evolutionary analyses were applied using MEGAx tools. Results: The strain sequenced in this study belongs to a very virulent Infectious Bursal Disease Virus (vvIBDV) as the DNA and phylogenetic analysis of VP1 and VP2 gene sequences showed a mutual clustering with similar sequences belonging to vvIBDV genogroup 3. Analyses of the hyper variable region of VP2 gene (hvVP2) of IBDV isolates from Iraq indicates a presence of sequence diversity. Interestingly, the two vaccine strains Ventri IBDV Plus and ABIC MB71 that showed the highest sequence similarity to the local isolates in the hvVP2 region are not used in vaccination routine against IBDV in Iraq. Conclusion: Sequences of vvIBDV in Iraq are diverse. Remarkably, some of the available vaccine strains show high sequence similarity with local strains in Iraq; however, they are not included in the routine vaccination programs. Analysis of more samples involving more geographical regions is needed to draw a detailed map of antigenic diversity of IBDV in Iraq.

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30

Billari, Francesco C. "Sequence Analysis in Demographic Research." Canadian Studies in Population 28, no. 2 (December 31, 2001): 439. http://dx.doi.org/10.25336/p6g30c.

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This paper examines the salient features of sequence analysis in demographic research. The new approach allows a holistic perspective on life course analysis, and is based on a representation of lives as sequences of states. Some of the methods for analysing such data are sketched, from complex description to optimal matching to monothetic divisive algorithms. After a short illustration of a demographically relevant example, the needs in terms of data collection and the opportunities of applying the same approach to synthetic data are discussed.

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31

Caflisch, Russel E. "Monte Carlo and quasi-Monte Carlo methods." Acta Numerica 7 (January 1998): 1–49. http://dx.doi.org/10.1017/s0962492900002804.

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Monte Carlo is one of the most versatile and widely used numerical methods. Its convergence rate, O(N−1/2), is independent of dimension, which shows Monte Carlo to be very robust but also slow. This article presents an introduction to Monte Carlo methods for integration problems, including convergence theory, sampling methods and variance reduction techniques. Accelerated convergence for Monte Carlo quadrature is attained using quasi-random (also called low-discrepancy) sequences, which are a deterministic alternative to random or pseudo-random sequences. The points in a quasi-random sequence are correlated to provide greater uniformity. The resulting quadrature method, called quasi-Monte Carlo, has a convergence rate of approximately O((logN)kN−1). For quasi-Monte Carlo, both theoretical error estimates and practical limitations are presented. Although the emphasis in this article is on integration, Monte Carlo simulation of rarefied gas dynamics is also discussed. In the limit of small mean free path (that is, the fluid dynamic limit), Monte Carlo loses its effectiveness because the collisional distance is much less than the fluid dynamic length scale. Computational examples are presented throughout the text to illustrate the theory. A number of open problems are described.

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32

Feng, Chunyu, Yuting Liu, Guangqi Lyu, Songyang Shang, Hongyue Xia, Junpeng Zhang, David M. Irwin, Zhe Wang, and Shuyi Zhang. "Adaptive Evolution of the Fox Coronavirus Based on Genome-Wide Sequence Analysis." BioMed Research International 2022 (April 13, 2022): 1–8. http://dx.doi.org/10.1155/2022/9627961.

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Purpose. To report the first complete fox coronavirus (CoV) genome sequence obtained through genome-wide amplifications and to understand the adaptive evolution of fox CoV. Methods. Anal swab samples were collected from 35 foxes to detect the presence of CoV and obtain the virus sequence. Phylogenetic analysis was conducted using MrBayes. The possibility of recombination within these sequences was assessed using GARD. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Data Monkey platforms. Results. Of the 35 samples, two were positive, and complete genome sequences for the viruses were obtained. Phylogenetic analysis, using Bayesian methods, of these sequences, together with other CoV sequences, revealed that the fox CoV sequences clustered with canine coronavirus (CCoV) sequences, with sequences from other carnivores more distantly related. In contrast to the feline, ferret and mink CoV sequences that clustered into species-specific clades, the fox CoV fell within the CCoV clade. Minimal evidence for recombination was found among the sequences. A total of 7, 3, 14, and 2 positively selected sites were identified in the M, N, S, and 7B genes, respectively, with 99, 111, and 581 negatively selected sites identified in M, N, and S genes, respectively. Conclusion. The complete genome sequence of fox CoV has been obtained for the first time. The results suggest that the genome sequence of fox CoV may have experienced adaptive evolution in the genes replication, entry, and virulence. The number of sites in each gene that experienced negative selection is far greater than the number that underwent positive selection, suggesting that most of the sequence is highly conserved and important for viral survive. However, positive selection at a few sites likely aided these viruses to adapt to new environments.

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33

Liu, Wen-li, and Qing-biao Wu. "Analysis method and algorithm design of biological sequence problem based on generalized k-mer vector." Applied Mathematics-A Journal of Chinese Universities 36, no. 1 (March 2021): 114–27. http://dx.doi.org/10.1007/s11766-021-4033-x.

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AbstractK-mer can be used for the description of biological sequences and k-mer distribution is a tool for solving sequences analysis problems in bioinformatics. We can use k-mer vector as a representation method of the k-mer distribution of the biological sequence. Problems, such as similarity calculations or sequence assembly, can be described in the k-mer vector space. It helps us to identify new features of an old sequence-based problem in bioinformatics and develop new algorithms using the concepts and methods from linear space theory. In this study, we defined the k-mer vector space for the generalized biological sequences. The meaning of corresponding vector operations is explained in the biological context. We presented the vector/matrix form of several widely seen sequence-based problems, including read quantification, sequence assembly, and pattern detection problem. Its advantages and disadvantages are discussed. Also, we implement a tool for the sequence assembly problem based on the concepts of k-mer vector methods. It shows the practicability and convenience of this algorithm design strategy.

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34

Aghababyan, Ani, Taylor Martin, Phillip Janisiewicz, and Kevin Close. "Microgenetic Learning Analytics Methods: Hands-on Sequence Analysis Workshop Report." Journal of Learning Analytics 3, no. 3 (December 19, 2016): 96–114. http://dx.doi.org/10.18608/jla.2016.33.6.

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Learning analytics is an emerging discipline and, as such, it benefits from new tools and methodological approaches. This work reviews and summarizes our workshop on microgenetic data analysis techniques using R, held at the 2nd annual Learning Analytics Summer Institute in Cambridge, Massachusetts on June 30th, 2014. Specifically, this paper introduces educational researchers to our experience using data analysis techniques with the RStudio development environment to analyze temporal records of 52 elementary students’ affective and behavioral responses to a digital learning environment. In the RStudio development environment, we used methods such as hierarchical clustering and sequential pattern mining. We also used RStudio to create effective data visualizations of our complex data. The scope of the workshop, and this paper, assumes little prior knowledge of the R programming language, and thus covers everything from data import and cleanup to advanced microgenetic analysis techniques. Additionally, readers will be introduced to software setup, R data types, and visualizations. This paper not only adds to the toolbox for learning analytics researchers (particularly when analyzing time series data), but also shares our experience interpreting a unique and complex dataset.

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35

Gomes, A. R., S. Vinga, M. Zavolan, and H. de Lencastre. "Analysis of the Genetic Variability of Virulence-Related Loci in Epidemic Clones of Methicillin-Resistant Staphylococcus aureus." Antimicrobial Agents and Chemotherapy 49, no. 1 (January 2005): 366–79. http://dx.doi.org/10.1128/aac.49.1.366-379.2005.

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ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) isolates have previously been classified into major epidemic clonal types by pulsed-field gel electrophoresis in combination with multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec typing. We aimed to investigate whether genetic variability in potentially polymorphic domains of virulence-related factors could provide another level of differentiation in a diverse collection of epidemic MRSA clones. The target regions of strains representative of epidemic clones and genetically related methicillin-susceptible S. aureus isolates from the 1960s that were sequenced included the R domains of clfA and clfB; the D, W, and M regions of fnbA and fnbB; and three regions in the agr operon. Sequence variation ranged from very conserved regions, such as those for RNAIII and the agr interpromoter region, to the highly polymorphic R regions of the clf genes. The sequences of the clf R domains could be grouped into six major sequence types on the basis of the sequences in their 3′ regions. Six sequence types were also observed for the fnb sequences at the amino acid level. From an evolutionary point of view, it was interesting that a small DNA stretch at the 3′ clf R-domain sequence and the fnb sequences agreed with the results of MLST for this set of strains. In particular, clfB R-domain sequences, which had a high discriminatory capacity and with which the types distinguished were congruent with those obtained by other molecular typing methods, have potential for use for the typing of S. aureus. Clone- and strain-specific sequence motifs in the clf and fnb genes may represent useful additions to a typing methodology with a DNA array.

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36

Vanoli, Jacopo, Consuelo Rubina Nava, Chiara Airoldi, Andrealuna Ucciero, Virginio Salvi, and Francesco Barone-Adesi. "Use of State Sequence Analysis in Pharmacoepidemiology: A Tutorial." International Journal of Environmental Research and Public Health 18, no. 24 (December 20, 2021): 13398. http://dx.doi.org/10.3390/ijerph182413398.

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While state sequence analysis (SSA) has been long used in social sciences, its use in pharmacoepidemiology is still in its infancy. Indeed, this technique is relatively easy to use, and its intrinsic visual nature may help investigators to untangle the latent information within prescription data, facilitating the individuation of specific patterns and possible inappropriate use of medications. In this paper, we provide an educational primer of the most important learning concepts and methods of SSA, including measurement of dissimilarities between sequences, the application of clustering methods to identify sequence patterns, the use of complexity measures for sequence patterns, the graphical visualization of sequences, and the use of SSA in predictive models. As a worked example, we present an application of SSA to opioid prescription patterns in patients with non-cancer pain, using real-world data from Italy. We show how SSA allows the identification of patterns in prescriptions in these data that might not be evident using standard statistical approaches and how these patterns are associated with future discontinuation of opioid therapy.

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37

Pruksakorn, Sumalee, Nopporn Sittisombut, Charlie Phornphutkul, Chulabhorn Pruksachatkunakorn, Michael F. Good, and Evelyn Brandt. "Epidemiological Analysis of Non-M-Typeable Group A Streptococcus Isolates from a Thai Population in Northern Thailand." Journal of Clinical Microbiology 38, no. 3 (2000): 1250–54. http://dx.doi.org/10.1128/jcm.38.3.1250-1254.2000.

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Infection with group A streptococci (GAS) can lead to the development of severe postinfectious sequelae such as rheumatic fever (RF). In Thailand, RF and rheumatic heart disease (RHD) remain important health problems. More than 80% of GAS circulating in this population are non-M antigen typeable by conventional M serotyping methods. In this study, we determine the M protein sequence types of GAS isolates found in northern Thailand. The emm genes from 53 GAS isolates, collected between 1985 and 1995 from individuals with pharyngitis, impetigo, acute RF (ARF), RHD, or meningitis as well as from individuals without infections, were amplified by PCR and sequenced. Thirteen new sequence types that did not show homology to previously published sequences were characterized. Six of these sequence types could be isolated from both skin and throat sites of impetigo and pharyngitis/ARF patients, respectively. In many cases we could not specifically differentiate skin strains or throat strains that could be associated with ARF or acute glomerulonephritis. Antigenic variations in the emm gene of the isolates investigated, compared to published M protein sequences, were predominantly due to point mutations, small deletions, and insertions in the hypervariable region. One group of isolates with homology to M44 exhibited corrected frameshift mutations. A new M type isolated from an RHD patient exhibited nucleotide sequence corresponding to the N terminus of M58 and the C terminus of M25, suggesting that recombination between the two types may have occurred. This study provided epidemiological data relating to GAS endemic to northern Thailand which could be useful for identification of vaccine candidates in a specific region of endemicity.

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38

Shahruddin, Munawar Zaman, Mohamad Hamidi Asri, Rohani Mohd Zin, Ahmad Nafais Rahimi, Muhammad Afiq Zubir, Muhammad Fakhrul Islam Zahran, Norazana Ibrahim, and Mohd Kamaruddin Abd. Hamid. "Natural gas liquid (NGL) distillation process using driving force and thermal pinch analysis methods: Energy and economic assessment." Malaysian Journal of Chemical Engineering and Technology (MJCET) 3, no. 2 (December 31, 2020): 18. http://dx.doi.org/10.24191/mjcet.v3i2.10996.

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Distillation column is one of the effective unit operations that is commonly used to separate chemical mixtures. The only drawback of this separation process is its huge energy consumption especially for a multicomponent separation process which involves a series of distillation columns. Therefore, an optimal sequence must be determined to address the issue. This research proposes the methodology to determine the optimal sequence of distillation columns by using driving force method. Then, thermal pinch analysis is applied to obtain further energy saving in the process. The case study selected is a distillation process to recover 5-component of natural gas liquid (NGL) mixture. Based on the input data, the driving force sequence is determined first and simulated together with a conventional sequence (direct sequence). Then, the extracted data from the simulation will be used for thermal pinch analysis via problem table algorithm (PTA). From the results of PTA, energy consumption between both sequences were compared including the energy consumption before and after the thermal pinch analysis. In addition, economic analysis has been performed as well to indicate which sequence has lower capital and operating costs based on the proposed heat exchanger network (HEN). According to the results, the combination of the driving force and thermal pinch analysis methods has successfully recorded 48% of energy savings and operating cost, and 58.2% capital cost saving compared to the conventional sequence (direct sequence). Therefore, it can be said that the proposed framework has a great potential to be employed towards the process and economic feasible distillation process.

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39

Bucerzan, Dominic, Mihaela Crăciun, Violeta Chiș, and Crina Rațiu. "Stream Ciphers Analysis Methods." International Journal of Computers Communications & Control 5, no. 4 (November 1, 2010): 483. http://dx.doi.org/10.15837/ijccc.2010.4.2506.

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The purpose of this paper is to present and to discuss analysis methods applied in symmetric cryptography, especially on stream ciphers. The tests were made on some algorithms and also on the personal symmetric cryptographic algorithm, HENKOS, based on a pseudorandom number generator. The test confirms that the algorithm appears to be secure and fast. The paper describes first the main parts of the cryptosystem, its implementation and different analysis methods. The code is written in the C/C++ language. The software application and the tests applied were processed on a PC computer. The quality analysis presents the results of many classical statistical tests, comparing some algorithms based especially on pseudo random number generators. The tests use standard sequence of 12.5 MB resulted from some test generators. The main part of the work presents selected results for the most important statistical tests like: FIPS 1401, FIPS 1402 , ENT tests, Diehard battery of tests, NIST Statistical Test Suite. The final question is: are these tests enough to certifie the quality of a tested algorithm?

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40

Regmi, Samundra, Ioannis K. Argyros, Stepan Shakhno, and Halyna Yarmola. "Unified Convergence Criteria of Derivative-Free Iterative Methods for Solving Nonlinear Equations." Computation 11, no. 3 (March 1, 2023): 49. http://dx.doi.org/10.3390/computation11030049.

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A local and semi-local convergence is developed of a class of iterative methods without derivatives for solving nonlinear Banach space valued operator equations under the classical Lipschitz conditions for first-order divided differences. Special cases of this method are well-known iterative algorithms, in particular, the Secant, Kurchatov, and Steffensen methods as well as the Newton method. For the semi-local convergence analysis, we use a technique of recurrent functions and majorizing scalar sequences. First, the convergence of the scalar sequence is proved and its limit is determined. It is then shown that the sequence obtained by the proposed method is bounded by this scalar sequence. In the local convergence analysis, a computable radius of convergence is determined. Finally, the results of the numerical experiments are given that confirm obtained theoretical estimates.

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41

Macas, Jiří, Pavel Neumann, Petr Novák, and Jiming Jiang. "Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data." Bioinformatics 26, no. 17 (July 8, 2010): 2101–8. http://dx.doi.org/10.1093/bioinformatics/btq343.

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Abstract Motivation: Satellite DNA makes up significant portion of many eukaryotic genomes, yet it is relatively poorly characterized even in extensively sequenced species. This is, in part, due to methodological limitations of traditional methods of satellite repeat analysis, which are based on multiple alignments of monomer sequences. Therefore, we employed an alternative, alignment-free, approach utilizing k-mer frequency statistics, which is in principle more suitable for analyzing large sets of satellite repeat data, including sequence reads from next generation sequencing technologies. Results: k-mer frequency spectra were determined for two sets of rice centromeric satellite CentO sequences, including 454 reads from ChIP-sequencing of CENH3-bound DNA (7.6 Mb) and the whole genome Sanger sequencing reads (5.8 Mb). k-mer frequencies were used to identify the most conserved sequence regions and to reconstruct consensus sequences of complete monomers. Reconstructed consensus sequences as well as the assessment of overall divergence of k-mer spectra revealed high similarity of the two datasets, suggesting that CentO sequences associated with functional centromeres (CENH3-bound) do not significantly differ from the total population of CentO, which includes both centromeric and pericentromeric repeat arrays. On the other hand, considerable differences were revealed when these methods were used for comparison of CentO populations between individual chromosomes of the rice genome assembly, demonstrating preferential sequence homogenization of the clusters within the same chromosome. k-mer frequencies were also successfully used to identify and characterize smRNAs derived from CentO repeats. Contact: macas@umbr.cas.cz Supplementary information: Supplementary data are available at Bioinformatics online.

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42

Kwok, Anita Y. C., Jason T. Wilson, Michael Coulthart, Lai-King Ng, Lucy Mutharia, and Anthony W. Chow. "Phylogenetic study and identification of human pathogenicVibriospecies based on partialhsp60 gene sequences." Canadian Journal of Microbiology 48, no. 10 (October 1, 2002): 903–10. http://dx.doi.org/10.1139/w02-089.

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The use of hsp60 gene sequences for phylogenetic study and identification of pathogenic marine vibrios was investigated. A 600-bp partial hsp60 gene was amplified by PCR and sequenced from 29 strains representing 15 Vibrio species within the family Vibrionaceae. Sequence comparison of the amplified partial hsp60 gene revealed 7182% sequence identity among different Vibrio species and 96100% sequence identity among epidemiologically distinct strains with the same species designation. This degree of discrimination allows unambiguous differentiation of all Vibrio species included in the current study from each other, as well as from Aeromonas hydrophila and Plesiomonas shigelloides, which are often misidentified as Vibrio species by conventional biochemical methods. Based on the hsp60 gene sequences, two previously unidentified shrimp isolates were found to be more closely related to Vibrio alginolyticus (9394% sequence identity) than to Vibrio parahaemolyticus (89% sequence identity), whereas 16S rRNA gene analysis was unable to differentiate among these closely related species (9597% sequence identity). Our results indicate that the hsp60 gene may be a useful alternative target for phylogenetic analysis and species identification of marine Vibrios to complement more conventional identification systems.Key words: Vibrio, hsp60, 16S rRNA, phylogenetic analysis, species identification.

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43

Zhang, Shao Xuan, Xin Rui Liu, Bo Chuan Wang, Yun Hui Ling, De Jun Sun, and Guang Zhu Lin. "Comparison of the ITS Sequences of 5 Common Potentilla Species in Jilin Province of China." Advanced Materials Research 554-556 (July 2012): 1690–93. http://dx.doi.org/10.4028/www.scientific.net/amr.554-556.1690.

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To find the differences in the internal transcribed spacer(ITS) sequences and provide scientific data for the authentication of Potentilla chinensis and its related species, we extracted the genome DNA from the leaves of 5 common Potetilla species in Jilin Province, amplified the ITS region using ITS universal primers of angiosperm, and sequenced the purified PCR products directly. Polymorphism of ITS sequences was found within P. chinensis and the sequence data suggested that our samples of this species might be related to hybridization. Other 4 species showed intraspecies-stability in ITS sequence. The ITS sequences of these 5 Potentilla species are significantly different. So ITS sequence analysis and other methods derived from it can be used in authentication of Potentilla.

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44

Olori, Jennifer C. "Ontogenetic sequence reconstruction and sequence polymorphism in extinct taxa: an example using early tetrapods (Tetrapoda: Lepospondyli)." Paleobiology 39, no. 3 (2013): 400–428. http://dx.doi.org/10.1666/12031.

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Ontogenetic sequence reconstruction is challenging particularly for extinct taxa because of when, where, and how fossils preserve. Different methods of reconstruction exist, but the effects of preservational bias, the applicability of size-independent methods, and the prevalence of sequence polymorphism (intraspecific variation) remain unexplored for paleontological data. Here I compare five different methods of ontogenetic sequence reconstruction and their effects on the detection of sequence polymorphism, using a large collection of the extinct vertebrates Microbrachis pelikani and Hyloplesion longicostatum. The postcranial ossification sequences presented here for those taxa are the first examples known for extinct lepospondyls. Sequences were reconstructed according to skull length, trunk length, increasing number of ontogenetic events, majority-rule consensus, and Ontogenetic Sequence Analysis (OSA). Results generally were in agreement, demonstrating that paleontological data may be used to robustly reconstruct developmental patterns. When reconstructing sequences based on fossils, size-based methods and OSA are more objective and less dependent on preservational bias than other techniques. Apart from the other methods, OSA also allows for statistical analysis of observed and predicted polymorphism. However, OSA requires a large sample size to yield meaningful results, and size-based methods are justified in paleontological studies when sample size is limited by poor preservation. Different methods of reconstruction detected different patterns of sequence polymorphism, although across all methods the magnitude of sequence variation for M. pelikani and H. longicostatum (1.3−3.4%) was within the lower range of values reported for extant vertebrates. Compared with other extinct and extant tetrapods, all sequence reconstruction methods consistently showed that M. pelikani and H. longicostatum exhibit advanced ossification of the pubis and delayed ossification of the scapula. However, the postcranial ossification sequences of these two taxa largely are congruent with those of other tetrapods, suggesting an underlying conservative ancestral pattern that evolved early in tetrapod history.

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45

Faria, José P., Miguel Rocha, Isabel Rocha, and Christopher S. Henry. "Methods for automated genome-scale metabolic model reconstruction." Biochemical Society Transactions 46, no. 4 (July 31, 2018): 931–36. http://dx.doi.org/10.1042/bst20170246.

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In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. Here, we are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.

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46

Li, Hsin Chieh, Jean-Philippe Bouchara, Mark Ming-Long Hsu, Richard Barton, Shuli Su, and Tsung Chain Chang. "Identification of dermatophytes by sequence analysis of the rRNA gene internal transcribed spacer regions." Journal of Medical Microbiology 57, no. 5 (May 1, 2008): 592–600. http://dx.doi.org/10.1099/jmm.0.47607-0.

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Identification of dermatophytes using the traditional method is sometimes problematic because of atypical microscopic or macroscopic morphology. The aim of this study was to evaluate the feasibility of using sequencing of the ribosomal internal transcribed spacer (ITS)1 and ITS2 regions for identification of 17 dermatophyte species. The ITS regions of 188 strains (62 reference strains and 126 clinical isolates) were amplified by PCR and sequenced. Species identification was made by sequence comparison with an in-house database comprising ITS sequences of type or neotype strains or by blast searches for homologous sequences in public databases. Strains producing discrepant results between conventional methods and ITS sequence analysis were analysed further by sequencing the D1–D2 domain of the large-subunit rRNA gene for species clarification. The identification rates by ITS1 and ITS2 sequencing were higher than 97 %. Based on reference sequences of type or neotype strains, it was noted that most strains of Trichophyton mentagrophytes were misidentifications of Trichophyton interdigitale. In addition, barcode sequences were present in species of the Microsporum canis complex and Trichophyton rubrum complex. These barcode sequences are useful for species delineation when the results of ITS sequencing are ambiguous. In conclusion, ITS sequencing provides a very accurate and useful method for the identification of dermatophytes.

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47

Datta, Sibnarayan, Reji Gopalakrishnan, Soumya Chatterjee, and Vijay Veer. "Phylogenetic Characterization of a Novel Insect-Specific Flavivirus Detected in a Culex Pool, Collected from Assam, India." Intervirology 58, no. 3 (2015): 149–54. http://dx.doi.org/10.1159/000381901.

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Objective: We report the phylogenetic characterization of a unique flavivirus sequence detected in a wild Culex tritaeniorhynchus mosquito pool, collected from the northeast Indian state of Assam. Methods: DNA and RNA were extracted from field-collected mosquito pools. Extracts were subjected to PCR and reverse transcriptase PCR amplification using universal and type-specific primers for direct detection of flavivirus-specific viral nucleic acids. An amplified flavivirus nonstructural protein 5 (NS5) genetic region was sequenced and BLAST searched, and phylogenetic analyses performed with reference sequences retrieved from GenBank. Results: Phylogenetic analyses revealed the sequence to be related to insect-specific flaviviruses (ISFs) of the genus Flavivirus, family Flaviviridae. Despite being related to the Palm Creek virus (PCV; an ISF very recently reported from Northern Australia), the present sequence (provisionally named Assam virus) was found to be highly divergent from PCV and other ISF sequences available in GenBank. The partial NS5 sequence analysis demonstrated low nucleotide sequence identity (66-77%) with known ISFs reported from other parts of the globe. Conclusion: Findings of this study suggest the presence of a candidate novel ISF - the first to be reported from India.

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Barton, Geoffrey J. "Protein Sequence Alignment Techniques." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 1998): 1139–46. http://dx.doi.org/10.1107/s0907444998008324.

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The basic algorithms for alignment of two or more protein sequences are explained. Alternative methods for scoring substitutions and gaps (insertions and deletions) are described, as are global and local alignment methods. Multiple alignment techniques are explained, including methods for profile comparison. A summary is given of programs for the alignment and analysis of protein sequences, either from sequence alone, or from three-dimensional structure.

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House, Brent L., Michael W. Mortimer, and Michael L. Kahn. "New Recombination Methods for Sinorhizobium meliloti Genetics." Applied and Environmental Microbiology 70, no. 5 (May 2004): 2806–15. http://dx.doi.org/10.1128/aem.70.5.2806-2815.2004.

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ABSTRACT The availability of bacterial genome sequences has created a need for improved methods for sequence-based functional analysis to facilitate moving from annotated DNA sequence to genetic materials for analyzing the roles that postulated genes play in bacterial phenotypes. A powerful cloning method that uses lambda integrase recombination to clone and manipulate DNA sequences has been adapted for use with the gram-negative α-proteobacterium Sinorhizobium meliloti in two ways that increase the utility of the system. Adding plasmid oriT sequences to a set of vehicles allows the plasmids to be transferred to S. meliloti by conjugation and also allows cloned genes to be recombined from one plasmid to another in vivo by a pentaparental mating protocol, saving considerable time and expense. In addition, vehicles that contain yeast Flp recombinase target recombination sequences allow the construction of deletion mutations where the end points of the deletions are located at the ends of the cloned genes. Several deletions were constructed in a cluster of 60 genes on the symbiotic plasmid (pSymA) of S. meliloti, predicted to code for a denitrification pathway. The mutations do not affect the ability of the bacteria to form nitrogen-fixing nodules on Medicago sativa (alfalfa) roots.

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50

Sherf, Z., P. Hopstone, G. Ostrovski, R. Klein, and D. Yehuda. "Problems in the Analysis of a Shock Sequence with Application to Gunfire Analysis and Simulation." Journal of the IEST 45, no. 1 (September 14, 2002): 161–77. http://dx.doi.org/10.17764/jiet.45.1.p2q37w26674406r8.

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In the planning of a laboratory simulation based on a transient sequence, non-conventional techniques must be applied to the analysis of the sequence, due to the non-stationary character of the signals. This paper deals with the specific analysis problems of a transient sequence. The RMS and spectral content analysis of a single transient elucidates the distortion in the characterization of the sequence, when stationary time-series analysis methods are implemented. The way this distortion affects the simulation of the sequence is presented next. From this presentation, it can be concluded that the best method for the laboratory simulation of a transient sequence is the application of a measured time-history, while preserving the statistical features of the sequence. This conclusion has been implemented in the planning of the laboratory simulation of a gunfire-generated sequence of transients, produced by a gun installed on a helicopter. Statistics of the maximum values of each transient were calculated, for the sequences measured under changing firing conditions. Based on these statistics and on the knowledge of the total number of rounds, the number of transients of different maxima during the entire life cycle could be evaluated. Also a life-cycle representative sequence that could be simulated by a shaker was generated. A second method for the gun firing sequence simulation was also tested. In this case, the shot with maximal peak value was used and the number of equivalent shocks representing the entire lifecycle calculated, using a fatigue accumulation model. The weakness of the method is in the fatigue model.

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