Identification of CPG island in DNA sequence using Labview

2016 ◽  
Author(s):  
S. Soni ◽  
D.K. Shakya
Keyword(s):  
Dna Sequence ◽  
Cpg Island

scholarly journals A DNA Sequence Based Polymer Model for Chromatin Folding

2021 ◽  
Vol 22 (3) ◽  
pp. 1328
Author(s):  
Rui Zhou ◽  
Yi Qin Gao
Keyword(s):  
Dna Sequence ◽  
Cpg Island ◽  
Coarse Grained ◽  
Chromosome Territories ◽  
Base Pairs ◽  
Single Chromosome ◽  
Power Law Decay ◽  
Multiple Length Scales ◽  
Spatial Domains ◽  
Chromatin Folding

The recent development of sequencing technology and imaging methods has provided an unprecedented understanding of the inter-phase chromatin folding in mammalian nuclei. It was found that chromatin folds into topological-associated domains (TADs) of hundreds of kilo base pairs (kbps), and is further divided into spatially segregated compartments (A and B). The compartment B tends to be located near to the periphery or the nuclear center and interacts with other domains of compartments B, while compartment A tends to be located between compartment B and interacts inside the domains. These spatial domains are found to highly correlate with the mosaic CpG island (CGI) density. High CGI density corresponds to compartments A and small TADs, and vice versa. The variation of contact probability as a function of sequential distance roughly follows a power-law decay. Different chromosomes tend to segregate to occupy different chromosome territories. A model that can integrate these properties at multiple length scales and match many aspects is highly desired. Here, we report a DNA-sequence based coarse-grained block copolymer model that considers different interactions between blocks of different CGI density, interactions of TAD formation, as well as interactions between chromatin and the nuclear envelope. This model captures the various single-chromosome properties and partially reproduces the formation of chromosome territories.

scholarly journals A Multifactorial Signature of DNA Sequence and Polycomb Binding Predicts Aberrant CpG Island Methylation

2008 ◽  
Vol 69 (1) ◽  
pp. 282-291 ◽  
Author(s):  
Michael T. McCabe ◽  
Eva K. Lee ◽  
Paula M. Vertino
Keyword(s):  
Dna Sequence ◽  
Cpg Island ◽  
Cpg Island Methylation

scholarly journals CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure

PLoS Genetics ◽  
2006 ◽  
Vol 2 (3) ◽  
pp. e26 ◽  
Author(s):  
Christoph Bock ◽  
Martina Paulsen ◽  
Sascha Tierling ◽  
Thomas Mikeska ◽  
Thomas Lengauer ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Cpg Island ◽  
Human Lymphocytes ◽  
Dna Structure ◽  
Cpg Island Methylation ◽  
Highly Correlated ◽  
Dna Sequence Repeats

scholarly journals CpG island methylation in human lymphocytes is highly correlated with DNA sequence patterns, repeat frequencies and predicted DNA structure

PLoS Genetics ◽  
2005 ◽  
Vol preprint (2006) ◽  
pp. e26 ◽  
Author(s):  
Christoph Bock ◽  
Martina Paulsen ◽  
Sascha Tierling ◽  
Thomas Mikeska ◽  
Thomas Lengauer ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Cpg Island ◽  
Human Lymphocytes ◽  
Dna Structure ◽  
Sequence Patterns ◽  
Cpg Island Methylation ◽  
Highly Correlated

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

Phylogenetic relationships ofSalvia(Lamiaceae) in China: Evidence from DNA sequence datasets

2012 ◽  
pp. n/a-n/a
Author(s):  
Qian-Quan Li ◽  
Min-Hui Li ◽  
Qing-Jun Yuan ◽  
Zhan-Hu Cui ◽  
Lu-Qi Huang ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships

Corrected DNA Sequence of the Platelet Glycoprotein IX Gene

1997 ◽  
Vol 77 (05) ◽  
pp. 1034-1035 ◽  
Author(s):  
Tomohiro Hayashi ◽  
Keijiroh Suzuki ◽  
Akito Yahagi ◽  
Jiroh Akiba ◽  
Katsushi Tajima ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Platelet Glycoprotein

The Conceptualist Ends of Writing and the End of Conceptualism

CounterText ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 63-77
Author(s):  
Louis Armand
Keyword(s):  
Dna Sequence ◽  
Life Form ◽  
The Sun

This essay examines the convergence of conceptualist poetics with evolutionary code as a form of ‘becoming alien’. The focus is Christian Bök's The Xenotext project: an attempt at translating a ‘short verse about language and genetics’, using a chemical alphabet, into a DNA sequence implanted into the genome of a polyextremophile bacterium capable of enduring conditions in outerspace. Bök describes the project as, ‘in effect, engineering a life-form so that it becomes not only a durable archive for storing a poem, but also as an operant machine for writing a poem – one that can persist on the planet until the sun itself explodes …’. The concrete, constraint-based character of Bök's project evokes a mode of writing between posthumanist aesthetics and a positivist grammatology by turns deconstructive and itself requiring of deconstruction.

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