Information theory for DNA sequencing: Part I: A basic model

2012 ◽  
Author(s):  
Abolfazl Motahari ◽  
Guy Bresler ◽  
David Tse
Keyword(s):  
Information Theory ◽  
Dna Sequencing ◽  
Basic Model ◽  
Sequencing Part

scholarly journals Argumentative Theory of probability in the philosophy of Science

2018 ◽  
Vol 225 (2) ◽  
pp. 425-450
Author(s):  
Dr. Karim Mousa Hussein Mezban
Keyword(s):  
Information Theory ◽  
Probability Theory ◽  
Twentieth Century ◽  
Philosophy Of Science ◽  
Induction Method ◽  
Contemporary Theory ◽  
Logical Probability ◽  
Classical Probability ◽  
Hans Reichenbach ◽  
Basic Model

     This research was devoted to elaborate various models of probability theory which is adopted by a number of philosophers of science in the twentieth century.  The debate between them about the validity of probability theory is shown through philosophical researches, the research is distributed to fifth sections which can be listed as follow: Part (1): The theory of classical probability (classical) has been devoted to knowledge of the basic model of probability theory. Part (2): the theory of repetitive probability adopted by the philosopher of science Hans Reichenbach to fill the lack of the model The basis of probability theory part (3): The theory of logical probability adopted by the philosopher of science Rudolf Carnab to fill the logical deficit in the theory of the repetitive probability of Rischenbach, and also included sparring between them. part(4): The theory of probability of vascular, divided into two parts: Section 4.a: Pragmatisms is adopted by philosopher Charles Pierce to enshrine pragmatism or tendency in the concept of probability. Section 4.b: Karl Popper's Probabilistic Probability Theory, in which he defended the inability of probability to justify the induction method. part(5): The theory of entropy probability, which was devoted to the contemporary theory of probability that took all previous models of probability according to information theory.

Highly accurate fluorogenic DNA sequencing with information theory–based error correction

2017 ◽  
Vol 35 (12) ◽  
pp. 1170-1178 ◽  
Author(s):  
Zitian Chen ◽  
Wenxiong Zhou ◽  
Shuo Qiao ◽  
Li Kang ◽  
Haifeng Duan ◽  
...  
Keyword(s):  
Information Theory ◽  
Dna Sequencing ◽  
Error Correction

scholarly journals Information theory, evolutionary innovations and evolvability

2017 ◽  
Vol 372 (1735) ◽  
pp. 20160416 ◽  
Author(s):  
Andreas Wagner
Keyword(s):  
Information Theory ◽  
Gene Regulation ◽  
Dna Sequencing ◽  
Information Content ◽  
High Throughput ◽  
Carbon Sources ◽  
Darwinian Evolution ◽  
Evolutionary Adaptation ◽  
Phenotypic Information ◽  
High Throughput Dna Sequencing

How difficult is it to ‘discover’ an evolutionary adaptation or innovation? I here suggest that information theory, in combination with high-throughput DNA sequencing, can help answer this question by quantifying a new phenotype's information content. I apply this framework to compute the phenotypic information associated with novel gene regulation and with the ability to use novel carbon sources. The framework can also help quantify how DNA duplications affect evolvability, estimate the complexity of phenotypes and clarify the meaning of ‘progress’ in Darwinian evolution. This article is part of the themed issue ‘Process and pattern in innovations from cells to societies’.

scholarly journals Identification of Pathogenic Genes of Nonsyndromic Hearing Loss in Uyghur Families Using Massively Parallel DNA Sequencing Technique

2018 ◽  
Vol 2018 ◽  
pp. 1-9
Author(s):  
Yu Chen ◽  
Yu Lu ◽  
Pilidong Kuyaxi ◽  
Jing Cheng ◽  
Juan Zhao ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Dna Sequencing ◽  
Frameshift Mutation ◽  
Massively Parallel ◽  
Pathogenic Genes ◽  
Sequencing Technique ◽  
Sequencing Part ◽  
The Common ◽  
Massively Parallel Dna Sequencing ◽  
Biallelic Mutations

We aim to identify the mutations of deafness genes using massively parallel DNA sequencing in the 12 Uyghur families. SNPscan method was used to screen against the 124 sites in the common deafness genes in probands. Subjects with SNPscan negativity were subject to massively parallel DNA sequencing for the sequencing of 97 genes known to be responsible for hearing loss. Eight families (66.7%) showed biallelic mutations in probands, including MYO15A mutation (6892C>T in J02 family, 9514C>T/7894G>T in J07 family, and 9514C>T in J16 family), MYO7A mutation (1258A>T in J03 family), TMC1 mutation (773G>A in J09 family and 1247T>G/1312G>A in J11 family), and PCDH15 mutation (4658delT in J08 and J13 families). Six novel types of mutation were identified including 6892C>T, 9514C>T/7894G>T, and 9514C>T in MYO15A gene, 1258A>T in MYO7A, 773G>A in TMC1, and 4658delT in PCDH15. The ratio of nonsense mutation and frameshift mutation was comparatively high. All these indicated that the mutation types reported in this study were rare. In conclusion, rare deafness genes were identified in the Uyghur families using massively parallel DNA sequencing, part of which were suggested to be related to the pathogenesis of the disease.

Imaging polymers, proteins and dna in aqueous solutions with the atomic force microscope

1989 ◽  
Vol 47 ◽  
pp. 32-33
Author(s):  
S.A.C. Gould ◽  
B. Drake ◽  
C.B. Prater ◽  
A.L. Weisenhorn ◽  
S.M. Lindsay ◽  
...  
Keyword(s):  
Amino Acids ◽  
Dna Sequencing ◽  
Aqueous Solutions ◽  
Atomic Force Microscope ◽  
Piezoelectric Crystal ◽  
Atomic Force ◽  
Structure Of Molecules ◽  
Optical Lever

The atomic force microscope (AFM) is an instrument that can be used to image many samples of interest in biology and medicine. Images of polymerized amino acids, polyalanine and polyphenylalanine demonstrate the potential of the AFM for revealing the structure of molecules. Images of the protein fibrinogen which agree with TEM images demonstrate that the AFM can provide topographical data on larger molecules. Finally, images of DNA suggest the AFM may soon provide an easier and faster technique for DNA sequencing.The AFM consists of a microfabricated SiO2 triangular shaped cantilever with a diamond tip affixed at the elbow to act as a probe. The sample is mounted on a electronically driven piezoelectric crystal. It is then placed in contact with the tip and scanned. The topography of the surface causes minute deflections in the 100 μm long cantilever which are detected using an optical lever.

Constructing and Deconstructing Concepts

2016 ◽  
Vol 63 (5) ◽  
pp. 249-262 ◽  
Author(s):  
Charles A. Doan ◽  
Ronaldo Vigo
Keyword(s):  
Information Theory ◽  
Model Performance ◽  
Unsupervised Classification ◽  
Family Resemblance ◽  
Category Membership ◽  
Formal Models ◽  
Human Beings ◽  
One Dimensional ◽  
Relational Patterns ◽  
Optimal Classification

Abstract. Several empirical investigations have explored whether observers prefer to sort sets of multidimensional stimuli into groups by employing one-dimensional or family-resemblance strategies. Although one-dimensional sorting strategies have been the prevalent finding for these unsupervised classification paradigms, several researchers have provided evidence that the choice of strategy may depend on the particular demands of the task. To account for this disparity, we propose that observers extract relational patterns from stimulus sets that facilitate the development of optimal classification strategies for relegating category membership. We conducted a novel constrained categorization experiment to empirically test this hypothesis by instructing participants to either add or remove objects from presented categorical stimuli. We employed generalized representational information theory (GRIT; Vigo, 2011b , 2013a , 2014 ) and its associated formal models to predict and explain how human beings chose to modify these categorical stimuli. Additionally, we compared model performance to predictions made by a leading prototypicality measure in the literature.

TB OR NOT TB?… THAT IS THE QUESTION: A RARE MYCOBACTERIUM (M. INTERMEDIUM) IDENTIFIED BY DNA SEQUENCING

2001 ◽  
Vol 28 (10) ◽  
pp. 549-554
Author(s):  
Ryan N. Cole ◽  
Stewart W. West ◽  
Christine L. Terrell ◽  
Glenn D. Roberts ◽  
Iftikhar Ahmed
Keyword(s):  
Dna Sequencing
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