scholarly journals Visualization for genomics: the Microbial Genome Viewer

2004 ◽  
Vol 20 (11) ◽  
pp. 1812-1814 ◽  
Author(s):  
R. Kerkhoven ◽  
F. H. J. van Enckevort ◽  
J. Boekhorst ◽  
D. Molenaar ◽  
R. J. Siezen
Keyword(s):  
Microbial Genome ◽  
Genome Viewer

Energy Department Expanding Microbial Genome Efforts

2007 ◽  
Vol 2 (4) ◽  
pp. 169-170
Author(s):  
Jeffrey L. Fox
Keyword(s):  
Microbial Genome

Exploring genomes with a game engine

2014 ◽  
Vol 169 ◽  
pp. 443-453 ◽  
Author(s):  
Jeremiah J. Shepherd ◽  
Lingxi Zhou ◽  
William Arndt ◽  
Yan Zhang ◽  
W. Jim Zheng ◽  
...  
Keyword(s):  
Real Time ◽  
Video Game ◽  
Linear Structure ◽  
Structural Data ◽  
Game Engine ◽  
3D Genome ◽  
Genome Viewer ◽  
A Genome ◽  
Visualization Techniques ◽  
Insight Into

More and more evidence indicates that the 3D conformation of eukaryotic genomes is a critical part of genome function. However, due to the lack of accurate and reliable 3D genome structural data, this information is largely ignored and most of these studies have to use information systems that view the DNA in a linear structure. Visualizing genomes in real time 3D can give researchers more insight, but this is fraught with hardware limitations since each element contains vast amounts of information that cannot be processed on the fly. Using a game engine and sophisticated video game visualization techniques enables us to construct a multi-platform real-time 3D genome viewer. The game engine-based viewer achieves much better rendering speed and can handle much larger amounts of data compared to our previous implementation using OpenGL. Combining this viewer with 3D genome models from experimental data could provide unprecedented opportunities to gain insight into the conformation–function relationships of a genome.

Bacillus minimum genome factory: effective utilization of microbial genome information

2007 ◽  
Vol 46 (3) ◽  
pp. 169 ◽  
Author(s):  
Katsuya Ozaki ◽  
Katsutoshi Ara ◽  
Kouji Nakamura ◽  
Kunio Yamane ◽  
Junichi Sekiguchi ◽  
...  
Keyword(s):  
Microbial Genome ◽  
Effective Utilization ◽  
Genome Information

scholarly journals Development of Microbial Genome-Probing Microarrays using Digital Multiple Displacement Amplification of Uncultivated Microbial Single Cells

2008 ◽  
Vol 42 (22) ◽  
pp. 8614-8614
Author(s):  
Ho-Won Chang ◽  
Youboong Sung ◽  
Kyoung-Ho Kim ◽  
Young-Do Nam ◽  
Seong Woon Roh ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Single Cells ◽  
Microbial Genome

scholarly journals The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

2015 ◽  
Vol 10 (1) ◽  
Author(s):  
Marcel Huntemann ◽  
Natalia N. Ivanova ◽  
Konstantinos Mavromatis ◽  
H. James Tripp ◽  
David Paez-Espino ◽  
...  
Keyword(s):  
Operating Procedure ◽  
Genome Annotation ◽  
Standard Operating Procedure ◽  
Microbial Genome ◽  
Annotation Pipeline ◽  
Standard Operating

Using the Integrated Genome Viewer to reveal amplicon‐derived polymorphism enriched at the phenylthiocarbamide locus in the teaching lab

2021 ◽  
Author(s):  
Eric D. Brenner ◽  
Paul E. Scheid ◽  
Justin DeGrazia ◽  
Alexa R. Geltzeiler ◽  
Manpreet S. Katari
Keyword(s):  
Genome Viewer

scholarly journals The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

2018 ◽  
Vol 35 (13) ◽  
pp. 2332-2334 ◽  
Author(s):  
Federico Baldini ◽  
Almut Heinken ◽  
Laurent Heirendt ◽  
Stefania Magnusdottir ◽  
Ronan M T Fleming ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbial Interactions ◽  
Microbial Genome ◽  
Metagenomic Data ◽  
Metabolic Interactions ◽  
Constraint Based Modeling ◽  
Genome Scale

Abstract Motivation The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes. Results To address this gap, we created a comprehensive toolbox to model (i) microbe–microbe and host–microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox. Availability and implementation The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.

Natural product discovery through microbial genome mining

2021 ◽  
Vol 60 ◽  
pp. 47-54
Author(s):  
Emma Kenshole ◽  
Marion Herisse ◽  
Michael Michael ◽  
Sacha J. Pidot
Keyword(s):  
Natural Product ◽  
Genome Mining ◽  
Microbial Genome ◽  
Natural Product Discovery

scholarly journals IMG ER: a system for microbial genome annotation expert review and curation

2009 ◽  
Vol 25 (17) ◽  
pp. 2271-2278 ◽  
Author(s):  
Victor M. Markowitz ◽  
Konstantinos Mavromatis ◽  
Natalia N. Ivanova ◽  
I-Min A. Chen ◽  
Ken Chu ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Microbial Genome ◽  
Expert Review
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