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cgDNA specifications


Unique identifier OMICS_05735
Name cgDNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for cgDNA

cgDNA citations


Quantifying the impact of simple DNA parameters on the cyclization J factor for single basepair addition families

Sci Rep
PMCID: 5861124
PMID: 29559729
DOI: 10.1038/s41598-018-22502-7

[…] hat matches the prediction of the more complicated model.As a proof-of-principle demonstration of this idea, consider the results shown in Fig.  showing Monte Carlo estimates of J computed within the cgDNA model. This model takes as input the N-basepair DNA sequence and outputs an intrinsic shape within a rigid-base model and a (12N − 6) × (12N − 6) stiffness matrix, whose nonzero entries involve […]


Hexavalent Chromium Reduction under Fermentative Conditions with Lactate Stimulated Native Microbial Communities

PLoS One
PMCID: 3871698
PMID: 24376771
DOI: 10.1371/journal.pone.0083909

[…] rRNA subunit of Bacteria and Archaea, 13 ml media samples were collected every week from bioreactor outflows, centrifuged and pellets were stored at −80°C until analysis. Total community genomic DNA (cgDNA) was extracted using the PowerSoil™ DNA Isolation Kit (Mo Bio Labs, Inc., Carlsbad, CA). Separate sets of primers targeting the V1-3 hyper variable regions of the SSU rRNA subunit of Bacteria an […]


Functional Genomic Analysis of Candida glabrata Macrophage Interaction: Role of Chromatin Remodeling in Virulence

PLoS Pathog
PMCID: 3420920
PMID: 22916016
DOI: 10.1371/journal.ppat.1002863

[…] ated their inability to replicate properly in THP-1 cells. Liquid growth assays revealed no significant differences in the growth profiles for any mutant compared to the wt in YPD and RPMI medium (). Cgdna2 mutant was exquisitely sensitive to methyl methane sulfonate (MMS), a DNA alkylating agent, while growth of Cgchz1 mutant was impaired on plates containing MMS, hydrogen peroxide (H2O2), campto […]

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cgDNA institution(s)
Section de Mathématiques, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

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