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Topological Pressure specifications

Information


Unique identifier OMICS_16944
Name Topological Pressure
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Rodents
    • Mus musculus

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Versioning


No version available

Maintainer


  • person_outline David Koslicki

Publication for Topological Pressure

Topological Pressure citations

 (3)
library_books

The Transcriptome of Streptococcus pneumoniae Induced by Local and Global Changes in Supercoiling

2017
Front Microbiol
PMCID: 5534458
PMID: 28824578
DOI: 10.3389/fmicb.2017.01447

[…] (). several genes from the up and down domains were present in most streptococci at equivalent positions. the greatest position conservation was observed in 40 genes near the ori, indicating strong topological pressure to maintain functionalities in this region. genes near the ori have high copy numbers () and show a peculiar pattern of nap binding (). moreover, seven clusters with conserved […]

library_books

How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles

2016
Sci Rep
PMCID: 4763241
PMID: 26903405
DOI: 10.1038/srep22033

[…] the cleavage of plasmid dna is observed by electrophoresis mobility in agarose gels. native plasmid dna has a negatively super-coiled structure. introducing single-stranded cleavage releases the topological pressure in the plasmid dna and convert it into loose circular one. the cleavages in both strands in a close vicinity convert the dna into a linear structure. the three types of dna […]

library_books

Symbolic Extensions Applied to Multiscale Structure of Genomes

2014
Acta Biotheor
PMCID: 4012164
PMID: 24728912
DOI: 10.1007/s10441-014-9215-y

[…] in the area of genetics and it is natural to compare the dna sequence to an element of a symbolic space. there have been several successful attempts in applying the theory of entropy or that of topological pressure in order to better understand the structure of dna (see e.g. koslicki ; koslicki and thompson and the references therein). especially, the interpretation of so-called invariant […]


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Topological Pressure institution(s)
Department of Mathematics, Oregon State University, Corvallis, OR, USA; Department of Mathematics, The Ohio State University, Columbus, OH, USA

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