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Application of information theory to DNA sequence analysis: A review

Ramón Román-Roldán, Pedro Bernaola-Galván, JoséL Oliver
1996 Pattern Recognition  
The analysis of DNA sequences through information theory methods is reviewed from the beginning in the 70s.  ...  The emerging interest concerning long-range correlations and the mosaic structure of DNA sequences is considered from our own point of view.  ...  Acknowledgements--This work was partially supported by grants TIC91-646 to R.R.R. and PB93-1152-CO2-01 to J.L.O. from the DGICYT of the Spanish Government.  ... 
doi:10.1016/0031-3203(95)00145-x fatcat:7b3vw2gvsrg63nsrmcxhawzyku

The field of biomedicine: a systematic review and meta-analysis

Xia Jiang, Auctores Publishing LLC
2020 Journal of Clinical Research and Reports  
Combining practical problems such as DNA sequence classification and infectious diseases, it explains the establishment and application of mathematical models, and introduces the specific steps of mathematical  ...  It also specifically introduces: DNA sequence classification model, infectious disease model, curative effect evaluation model, deterministic model and randomness model, and promotes in-depth research  ...  of Technology (BSQD2019054), Hubei Province, China.  ... 
doi:10.31579/2690-1919/098 fatcat:4kodaocgcvf7jh4owctmoqx6eu

A review of symbolic analysis of experimental data

C. S. Daw, C. E. A. Finney, E. R. Tracy
2003 Review of Scientific Instruments  
This review covers the group of data-analysis techniques collectively referred to as symbolization or symbolic time-series analysis.  ...  Symbolization involves transformation of raw time-series measurements (i.e., experimental signals) into a series of discretized symbols that are processed to extract information about the generating process  ...  Our objective in this review is to summarize recent developments in the application of a data-analysis technique referred to as symbolization or symbolic time-series analysis.  ... 
doi:10.1063/1.1531823 fatcat:blodbrarirdhzfby3g2ihxve6a

Bioinformatics Analysis on DNA Barcode Sequences for Species Identification: A Review

Huyen-Trang Vu, Ly Le
2019 Annual Research & Review in Biology  
Establishment of worldwide DNA library for barcoding is essential. There were previous reviews on screenings and applications of barcodes in different taxa.  ...  In contrast, in sequence-based methods each nucleotide site is considered as genetic information hence a sequence of nucleotide represents large data, which is highly specific and more stable than PCR  ...  Since each site of sequence is considered as a character in bioinformatics analysis, the sequence-based method gives more variable information.  ... 
doi:10.9734/arrb/2019/v34i130142 fatcat:fjp54jzzljbwxkbilifnw2m2ya

Microfluidic Devices for Forensic DNA Analysis: A Review

Brigitte Bruijns, Arian van Asten, Roald Tiggelaar, Han Gardeniers
2016 Biosensors  
Microfluidic devices may offer various advantages for forensic DNA analysis, such as reduced risk of contamination, shorter analysis time and direct application at the crime scene.  ...  In the forensic field, one may expect microfluidic technology to become particularly relevant for the analysis of biological traces containing human DNA.  ...  Acknowledgments: The authors would like to thank Dyonne Nijhuis for providing the SEM pictures of the swabs. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/bios6030041 pmid:27527231 pmcid:PMC5039660 fatcat:stamaayxljbknflcmhi5agfdwe

Fractal and multifractal analysis: A review

R. Lopes, N. Betrouni
2009 Medical Image Analysis  
The aim of this review is to explain and to categorize the various algorithms into groups and their application in the field of medical signal analysis.  ...  Application of this geometry relies heavily on the estimation of the fractal features. Various methods were proposed to estimate the fractal dimension or multifractal spectral of a signal.  ...  However, there has been no review pa-per to digest these different methods and their application.  ... 
doi:10.1016/j.media.2009.05.003 pmid:19535282 fatcat:7uolep6jqjccdkd3ehjv2zpvn4

A Brief Review: The Z-curve Theory and its Application in Genome Analysis

Ren Zhang, Chun-Ting Zhang
2014 Current Genomics  
Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.  ...  The Z-curve theory is a geometrical approach to genome analysis.  ...  ACKNOWLEDGEMENTS The authors cordially thank the students and staff in the laboratory for assistance during the course of Z-curve studies.  ... 
doi:10.2174/1389202915999140328162433 pmid:24822026 pmcid:PMC4009844 fatcat:hxgrpsn465hgfb4p2etxwflxuy

Novel Vaccine Design Based on Genomics Data Analysis-A Review

Guangli Lu, Sharui Shan, Bibi Zainab, Zainab Ayaz, Jialiang He, Zhenxing Xie, Umer Rashid, Dalin Zhang, Arshad Mehmood Abbasi
2020 Scandinavian Journal of Immunology  
Although immunization with genomics data is a successful approach, its advantages must be assessed case by case and its applicability depends on the nature of the agent to be immunized, the nature of the  ...  The aim of this review was to discuss the evolution of vaccines, their characteristics as well as limitations.  ...  This study was supported by the Foundation for Distinguished Young Talents in Higher Education of Guangdong, China (2017KQNCX109).  ... 
doi:10.1111/sji.12986 pmid:33043473 fatcat:ml7e5ciftrer7mh25rjav73g4u

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

O. Bonham-Carter, J. Steele, D. Bastola
2013 Briefings in Bioinformatics  
New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming.  ...  Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery.  ...  BBC by analysis of mutual information Mutual information is a tool from information theory, which measures the amount of common information (or interaction) between two entities. Liu et al.  ... 
doi:10.1093/bib/bbt052 pmid:23904502 pmcid:PMC4296134 fatcat:vlnvqzzwzreqjh3pqi26uxyud4

Metagenomic Analysis using Phylogenetic Placement – A Review of the First Decade [article]

Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera
2022 arXiv   pre-print
Phylogenetic placement constitutes a valuable analysis tool per se, but also entails a plethora of downstream tools to interpret its results.  ...  In particular, the goals of this review are (i) to motivate the usage of phylogenetic placement and illustrate some of its use cases, (ii) to outline the full workflow, from raw sequences to publishable  ...  Acknowledgments We wish to thank the Reviewers for the detailed and constructive comments that helped to improve this manuscript.  ... 
arXiv:2202.03534v2 fatcat:vo5uowvjyjd47icuv6z63owzte

Microsatellite Sequences of Mammals and Their Applications in Genome Analysis in Pigs - A Review

Rahul Behl, Neelam Sheoran, Jyotsna Behl, M. S. Tantia, R. K. Vijh
2002 Asian-Australasian Journal of Animal Sciences  
The microsatellites are the short tandem repeats of 1 to 6 bp long monomer sequences that are repeated several times.  ...  Based on the unique capability of alternating purine-pyrimidine residues to form Z-DNA, the possible role of the microsatellites in gene regulation has been proposed.  ...  The repetitive elements may be interspersed in the genome or may occur as tandem repeats Microsatellite Sequences of Mammals and Their Applications in Genome Analysis in Pigs -A Review (Schmid and Jelinek  ... 
doi:10.5713/ajas.2002.1822 fatcat:ny3z6kzqzfgj3h4vnloolcsjwa

Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review

Miguel A. Gutierrez-Reinoso, Pedro M. Aponte, Manuel Garcia-Herreros
2021 Animals  
The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding  ...  Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs.  ...  Conflicts of Interest: The authors participating in this review declare not to have conflicts of interest.  ... 
doi:10.3390/ani11030599 pmid:33668747 pmcid:PMC7996307 fatcat:xerpvj6hlfhtlp6iwxqlw2fqqq

A Review on Clinical Data Mining

Taranath N.L
2016 International Journal Of Engineering And Computer Science  
The aim of this work is to provide a review on the foundation principles of mining clinical dataset, and present the findings and results of past researches on utilizing data mining techniques to mine  ...  The scope of this article is to present a brief report on preceding investigations made in the sphere of mining clinical data, the techniques applied and the conclusions recounted.  ...  DNA Sequence Analysis for Genetic Marker Detection Data mining techniques have proven to produce improvement in the analysis, classification of the affection status of more individuals and by locating  ... 
doi:10.18535/ijecs/v5i8.12 fatcat:qmz4ihenlzgsblbynlk3qcirxq

Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade

Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera
2022 Frontiers in Bioinformatics  
Phylogenetic placement constitutes a valuable analysis tool per se, but also entails a plethora of downstream tools to interpret its results.  ...  Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing.  ...  ACKNOWLEDGMENTS We wish to thank the Reviewers, as well as Guido Grimm, for the detailed and constructive comments that helped to improve this manuscript.  ... 
doi:10.3389/fbinf.2022.871393 fatcat:fph6gljpc5d75h3sun7xazmg6q

Alignment-free sequence comparison--a review

S. Vinga, J. Almeida
2003 Bioinformatics  
A variety of theoretical foundations are being used to derive alignment-free methods that overcome this limitation.  ...  The formulation of alternative metrics for dissimilarity between sequences and their algorithmic implementations are reviewed.  ...  ACKNOWLEDGEMENTS The authors thankfully acknowledge the financial support by grants SFRH/BD/3134/2000 and Sapiens/34794/99 of Fundação para a Ciência e Tecnologia of the Portuguese Ministry of Science  ... 
doi:10.1093/bioinformatics/btg005 pmid:12611807 fatcat:n5nv22jgwvbhtphlzts3j54xty
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