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Relevant bibliographies by topics / Nucleotide sequence – Statistical methods

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Academic literature on the topic 'Nucleotide sequence – Statistical methods'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 February 2022

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Journal articles on the topic "Nucleotide sequence – Statistical methods"

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Demongeot, Jacques, and Alexandra Henrion-Caude. "Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life." Biology 9, no. 5 (2020): 88. http://dx.doi.org/10.3390/biology9050088.

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(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life through the evolutionary dynamics of RNA populations. (2) Methods: By performing a step-by-step computation of the smallest possible hairpin/ring RNA sequences compatible with building up a variety of peptides of the primitive network, we inferred the sequence of a singu

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Yang, Z., S. Kumar, and M. Nei. "A new method of inference of ancestral nucleotide and amino acid sequences." Genetics 141, no. 4 (1995): 1641–50. http://dx.doi.org/10.1093/genetics/141.4.1641.

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Abstract A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozy

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Farkaš, Tomáš, Jozef Sitarčík, Broňa Brejová, and Mária Lucká. "SWSPM: A Novel Alignment-Free DNA Comparison Method Based on Signal Processing Approaches." Evolutionary Bioinformatics 15 (January 2019): 117693431984907. http://dx.doi.org/10.1177/1176934319849071.

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Computing similarity between 2 nucleotide sequences is one of the fundamental problems in bioinformatics. Current methods are based mainly on 2 major approaches: (1) sequence alignment, which is computationally expensive, and (2) faster, but less accurate, alignment-free methods based on various statistical summaries, for example, short word counts. We propose a new distance measure based on mathematical transforms from the domain of signal processing. To tolerate large-scale rearrangements in the sequences, the transform is computed across sliding windows. We compare our method on several dat

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Diancourt, Laure, Virginie Passet, Christian Chervaux, Peggy Garault, Tamara Smokvina, and Sylvain Brisse. "Multilocus Sequence Typing of Lactobacillus casei Reveals a Clonal Population Structure with Low Levels of Homologous Recombination." Applied and Environmental Microbiology 73, no. 20 (2007): 6601–11. http://dx.doi.org/10.1128/aem.01095-07.

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ABSTRACT Robust genotyping methods for Lactobacillus casei are needed for strain tracking and collection management, as well as for population biology research. A collection of 52 strains initially labeled L. casei or Lactobacillus paracasei was first subjected to rplB gene sequencing together with reference strains of Lactobacillus zeae, Lactobacillus rhamnosus, and other species. Phylogenetic analysis showed that all 52 strains belonged to a single compact L. casei-L. paracasei sequence cluster, together with strain CIP107868 (= ATCC 334) but clearly distinct from L. rhamnosus and from a clu

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Xia, Xuhua. "Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction." Scientifica 2012 (2012): 1–15. http://dx.doi.org/10.6064/2012/917540.

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Position weight matrix (PWM) is not only one of the most widely used bioinformatic methods, but also a key component in more advanced computational algorithms (e.g., Gibbs sampler) for characterizing and discovering motifs in nucleotide or amino acid sequences. However, few generally applicable statistical tests are available for evaluating the significance of site patterns, PWM, and PWM scores (PWMS) of putative motifs. Statistical significance tests of the PWM output, that is, site-specific frequencies, PWM itself, and PWMS, are in disparate sources and have never been collected in a single

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Pinheiro, M., V. Afreixo, G. Moura, A. Freitas, M. A. S. Santos, and J. L. Oliveira. "Statistical, Computational and Visualization Methodologies to Unveil Gene Primary Structure Features." Methods of Information in Medicine 45, no. 02 (2006): 163–68. http://dx.doi.org/10.1055/s-0038-1634061.

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Summary Objectives: Gene sequence features such as codon bias, codon context, and codon expansion (e.g. tri-nucleotide repeats) can be better understood at the genomic scale level by combining statistical methodologies with advanced computer algorithms and data visualization through sophisticated graphical interfaces. This paper presents the ANACONDA system, a bioinformatics application for gene primary structure analysis. Methods: Codon usage tables using absolute metrics and software for multivariate analysis of codon and amino acid usage are available in public databases. However, they do n

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Bilhère, Eric, Patrick M. Lucas, Olivier Claisse, and Aline Lonvaud-Funel. "Multilocus Sequence Typing of Oenococcus oeni: Detection of Two Subpopulations Shaped by Intergenic Recombination." Applied and Environmental Microbiology 75, no. 5 (2008): 1291–300. http://dx.doi.org/10.1128/aem.02563-08.

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ABSTRACT Oenococcus oeni is the acidophilic lactic acid bacterial species most frequently associated with malolactic fermentation of wine. Since the description of the species (formerly Leuconostoc oenos), characterization of indigenous strains and industrially produced cultures by diverse typing methods has led to divergent conclusions concerning the genetic diversity of strains. In the present study, a multilocus sequence typing (MLST) scheme based on the analysis of eight housekeeping genes was developed and tested on a collection of 43 strains of diverse origins. The eight targeted loci we

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Bedo, Justin, Benjamin Goudey, Jeremy Wazny, and Zeyu Zhou. "Information theoretic alignment free variant calling." PeerJ Computer Science 2 (July 25, 2016): e71. http://dx.doi.org/10.7717/peerj-cs.71.

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While traditional methods for calling variants across whole genome sequence data rely on alignment to an appropriate reference sequence, alternative techniques are needed when a suitable reference does not exist. We present a novel alignment and assembly free variant calling method based on information theoretic principles designed to detect variants have strong statistical evidence for their ability to segregate samples in a given dataset. Our method uses the context surrounding a particular nucleotide to define variants. Given a set of reads, we model the probability of observing a given nuc

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Timoshkina, Natalya N., Denis S. Kutilin, Inna A. Novikova, et al. "Features of iso-miR expression in colon tumor tissue." Journal of Clinical Oncology 38, no. 15_suppl (2020): e13518-e13518. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e13518.

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e13518 Background: With the advent of deep sequencing, enormous variability in miRNA biogenesis was detected, which means that many different sequences can potentially be generated from the same miRNA precursor, potentially having different targets and opposite changes in expression. These variable forms of micro-RNA that differ from the reference sequence are called iso-miR. To date, features of iso-miR expression have not been studied in patients with colorectal cancer (CRC). The aim of the study was to analyze the differential expression of iso-miR in the tumor and normal tissues of patient

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Abadi, Shiran, Oren Avram, Saharon Rosset, Tal Pupko, and Itay Mayrose. "ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning." Molecular Biology and Evolution 37, no. 11 (2020): 3338–52. http://dx.doi.org/10.1093/molbev/msaa154.

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Abstract Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they are not always feasible, and sometimes depend on preliminary assumptions which do not hold for sequence data. Moreover, although these methods are dedicated to revealing the processes that underlie the sequence data, they do not always produce the most accurate trees. Not

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Dissertations / Theses on the topic "Nucleotide sequence – Statistical methods"

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Didelot, Xavier. "Inference of bacterial microevolution from large scale DNA sequence datasets." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670148.

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Yu, Xuesong. "Statistical methods for analyzing genomic data with consideration of spatial structures /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9553.

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Lundberg, Johannes. "Phylogenetic Studies in the Euasterids II : with Particular Reference to Asterales and Escalloniaceae." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-5191-8/.

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Musgrave-Brown, Esther. "Development and application of methods for targeted DNA sequencing of pooled samples." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648613.

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Andrews, Daniel James. "Statistical models of PCR for quantification of target DNA by sequencing." Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708581.

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Holder, Mark Travis. "Using a complex model of sequence evolution to evaluate and improve phylogenetic methods." Access restricted to users with UT Austin EID Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3037500.

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Li, Yaoman, and 李耀满. "Efficient methods for improving the sensitivity and accuracy of RNA alignments and structure prediction." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/195977.

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RNA plays an important role in molecular biology. RNA sequence comparison is an important method to analysis the gene expression. Since aligning RNA reads needs to handle gaps, mutations, poly-A tails, etc. It is much more difficult than aligning other sequences. In this thesis, we study the RNA-Seq align tools, the existing gene information database and how to improve the accuracy of alignment and predict RNA secondary structure. The known gene information database contains a lot of reliable gene information that has been discovered. And we note most DNA align tools are well developed. The

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Besemer, John David. "Heuristic and self-training methods for improving gene prediction in prokaryotes." Diss., Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/25388.

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Mills, Ryan Edward. "New AB initio methods of small genome sequence interpretation." Diss., Available online, Georgia Institute of Technology, 2006, 2006. http://etd.gatech.edu/theses/available/etd-04062006-182528/.

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Thesis (Ph. D.)--Biomedical Engineering, Georgia Institute of Technology, 2006.<br>Tannenbaum, Allen, Committee Member ; Choi, Jung, Committee Member ; Borodovsky, Mark, Committee Chair ; Voit, Eberhard, Committee Member ; Lee, Eva, Committee Member.

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Lovmar, Lovisa. "Methods for Analysis of Disease Associated Genomic Sequence Variation." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4525.

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Books on the topic "Nucleotide sequence – Statistical methods"

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Probability models for DNA sequence evolution. Springer, 2002.

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Probability models for DNA sequence evolution. 2nd ed. Springer, 2008.

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Kasprzak, Marta. Combinatorial models and methods for reading genomic sequences. Wydawn. Politechniki Poznańskiej, 2004.

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Hidden Markov models for bioinformatics. Kluwer Academic Publishers, 2001.

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Alphey, Luke. DNA sequencing from experimental methods to bioinformatics. Springer, 1997.

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Munshi, Anjana. DNA sequencing: Methods and applications. InTech, 2012.

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Ophir, Frieder, and Martino Robert L, eds. High performance computational methods for biological sequence analysis. Kluwer Academic Publishers, 1996.

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RNA sequence, structure, and function: Computational and bioinformatic methods. Humana Press, 2014.

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Ancient DNA typing: Methods, strategies, and applications. Springer, 2003.

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RNA and DNA editing: Methods and protocols. Humana, 2011.

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Book chapters on the topic "Nucleotide sequence – Statistical methods"

1

Staden, Rodger. "Staden: Statistical and Structural Analysis of Nucleotide Sequences." In Computer Analysis of Sequence Data. Humana Press, 1994. http://dx.doi.org/10.1385/0-89603-276-0:69.

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Lange, Kenneth. "Sequence Analysis." In Mathematical and Statistical Methods for Genetic Analysis. Springer New York, 2002. http://dx.doi.org/10.1007/978-0-387-21750-5_13.

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Ewens, Warren J., and Gregory R. Grant. "The Analysis of One DNA Sequence." In Statistical Methods in Bioinformatics. Springer New York, 2001. http://dx.doi.org/10.1007/978-1-4757-3247-4_5.

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Syvänen, A. C., and H. Söderlund. "Nucleotide Sequence Determination As a Diagnostic Tool." In Rapid Methods and Automation in Microbiology and Immunology. Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76603-9_4.

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Liu, Jun S., and T. Logvinenko. "Bayesian Methods in Biological Sequence Analysis." In Handbook of Statistical Genetics. John Wiley & Sons, Ltd, 2008. http://dx.doi.org/10.1002/9780470061619.ch3.

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Susko, Edward, and Andrew J. Roger. "Statistical Analysis of Expressed Sequence Tags." In Methods in Molecular Biology. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-136-3_13.

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Smita, Suchi, Krishna P. Singh, Bashir A. Akhoon, and Shailendra K. Gupta. "Biological Sequence Analysis: Algorithms and Statistical Methods." In Springer Protocols Handbooks. Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-34410-7_20.

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Chatenay, Didier, Simona Cocco, Benjamin Greenbaum, Rémi Monasson, and Pierre Netter. "Evolutionary Constraints on Coding Sequences at the Nucleotidic Level: A Statistical Physics Approach." In Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-61569-1_18.

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Chorostecki, Uciel, Jesse R. Willis, Ester Saus, and Toni Gabaldon. "Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1307-8_4.

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AbstractRNA molecules play important roles in almost every cellular process, and their functions are mediated by their sequence and structure. Determining the secondary structure of RNAs is central to understanding RNA function and evolution. RNA structure probing techniques coupled to high-throughput sequencing allow determining structural features of RNA molecules at transcriptome-wide scales. Our group recently developed a novel Illumina-based implementation of in vitro parallel probing of RNA structures called nextPARS.Here, we describe a protocol for the computation of the nextPARS scores and their use to obtain the structural profile (single- or double-stranded state) of an RNA sequence at single-nucleotide resolution.

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Kalkkinen, Nisse. "Radio-Sequence Analysis; an Ultra-Sensitive Method to Align Protein and Nucleotide Sequences." In Advanced Methods in Protein Microsequence Analysis. Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-71534-1_16.

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Conference papers on the topic "Nucleotide sequence – Statistical methods"

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Aldwairi, Tamer, Bindu Nanduri, Mahalingam Ramkumar, Dilip Gautam, Michael Johnson, and Andy Perkins. "Statistical Methods for Ambiguous Sequence Mappings." In BCB'13: ACM-BCB2013. ACM, 2013. http://dx.doi.org/10.1145/2506583.2506678.

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Mahalakshmi, T., and J. Sajeev. "Hub chacterization from sequence information using statistical methods." In 2011 IEEE Recent Advances in Intelligent Computational Systems (RAICS). IEEE, 2011. http://dx.doi.org/10.1109/raics.2011.6069299.

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Kopina, M. B., O. V. Sinkevich, and T. A. Surina. "Species of the genus stagonosporopsis in the eaeu quarantine list, development of species identification methods." In Растениеводство и луговодство. Тимирязевская сельскохозяйственная академия, 2020. http://dx.doi.org/10.26897/978-5-9675-1762-4-2020-108.

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The article presents the results of the study of the phytopathological condition of plantations potatoes, cut and potted chrysanthemums. Descriptions of quarantine and non-quarantine fungi species isolated from plants are given. Data on species identification of micromycetes by morphological characteristics and nucleotide sequence decoding are specified.

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Alrwashdeh, Mohammad, Jian Kai Yu, Aniseh Abdalla, and Kan Wang. "Nuclear Data Statistical Treatment." In 2013 21st International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/icone21-16790.

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Several methods have been developed in order to evaluate the best fit for nuclear data parameters, these methods relies on sequence logical steps should be followed to get accurate and reliable results, it subdivided into: (1) the physical model have been used (2) data types (3) statistical methods (4) problems. This paper will discuss the statistical methods used to evaluate the best fit for the nuclear data. The difficulty in finding a real and reasonable solution to the fitting of data can be made easier by choosing the right fitting method. Different methods will converge differently depen

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Orlov, Yurii Nikolaevich. "Language recognition methods and Voynich Manuscript analysis." In 4th International Conference “Futurity designing. Digital reality problems”. Keldysh Institute of Applied Mathematics, 2021. http://dx.doi.org/10.20948/future-2021-20.

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The statistical properties of letters frequencies in European literature texts are investigated. The determination of logarithmic dependence of letters sequence for one-languge and two-language texts are examined. The pare of languages are suggested for Voynich Manuscript. The internal structure of Manuscript is considered. The spectral portraits of two-letters distribution are constructed.

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Liu, Shengli, Yongtu Liang, Xiao Wang, and Dong Han. "Statistical Analyses of Incidents on Onshore Hazardous Liquid Pipelines Based on PHMSA Database." In 2018 12th International Pipeline Conference. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/ipc2018-78528.

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To improve the safety of a pipeline system, engineers use different methods to diagnose the hazardous pipeline accidents. However, most methods ignore the time dependence of pipeline failures. The aim of this paper is to provide a novel approach to analyzing the hazardous liquid pipeline incidents’ temporal structure. The database of hazardous liquid spillages from the US between 2002 and 2018 is collected by the Pipeline Hazardous Material Safety Administration of the US Department of Transportation. The result suggests that the whole oil pipeline incident sequence cannot be modeled as a Pois

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Xi, Zhimin, Byeng D. Youn, and Chao Hu. "Effective Random Field Characterization Considering Statistical Dependence for Probability Analysis and Design." In ASME 2010 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2010. http://dx.doi.org/10.1115/detc2010-29183.

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The Proper Orthogonal Decomposition (POD) method has been employed to extract the important signatures of the random field presented in an engineering product or process. Our preliminary study found that coefficients of the signatures are statistically uncorrelated but may be dependent. In general, the statistical dependence of the coefficients is ignored in the random field characterization for probability analysis and design. This paper thus proposes an effective approach to characterize the random field for probability analysis and design while accounting for the statistical dependence amon

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Lian, Huan, Jason Martz, Niket Prakash, and Anna Stefanopoulou. "Fast Computation of Combustion Phasing and its Influence on Classifying Random or Deterministic Patterns." In ASME 2015 Internal Combustion Engine Division Fall Technical Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/icef2015-1173.

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The classification between a sequence of highly variable combustion events that have an underlying deterministic pattern and a sequence of combustion events with similar level of variability but random characteristics is important for control of combustion phasing. In the case of high cyclic variation (CV) with underlying deterministic patterns, it is possible to apply closed loop combustion control on a cyclic-basis with a fixed mean value, such as injection timing in homogeneous charge compression ignition (HCCI) or spark timing in spark ignition (SI) applications, to contract the CV. In the

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Garbatov, Yordan, and C. Guedes Soares. "Spatial Corrosion Wastage Modelling of Steel Plates Subjected to Marine Environments." In ASME 2017 36th International Conference on Ocean, Offshore and Arctic Engineering. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/omae2017-61751.

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The objective of the present study is to analyse and identify the most suitable corrosion degradation model, fitted with real corrosion depth measurement data sets and to reproduce the corroded steel plate surface as a function of time and spatial distribution using advanced statistical methods. An approach for properly identifying the best fitted model to real corrosion depth measurement data sets is employed. A sequence dependent data analysis is performed based on the fast Fourier transform, which is used as an input for a random field modelling of the corroded steel plate surfaces.

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Huang, Xuancheng, Jiacheng Zhang, Zhixing Tan, et al. "Modeling Voting for System Combination in Machine Translation." In Twenty-Ninth International Joint Conference on Artificial Intelligence and Seventeenth Pacific Rim International Conference on Artificial Intelligence {IJCAI-PRICAI-20}. International Joint Conferences on Artificial Intelligence Organization, 2020. http://dx.doi.org/10.24963/ijcai.2020/511.

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System combination is an important technique for combining the hypotheses of different machine translation systems to improve translation performance. Although early statistical approaches to system combination have been proven effective in analyzing the consensus between hypotheses, they suffer from the error propagation problem due to the use of pipelines. While this problem has been alleviated by end-to-end training of multi-source sequence-to-sequence models recently, these neural models do not explicitly analyze the relations between hypotheses and fail to capture their agreement because

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