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KBase Narrative - Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures

Dataset ·
 [1];  [2];  [3];  [2];  [4];  [5];  [6];  [7];  [8];  [9]
  1. Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, NY, USA; Oak Ridge National Laboratory
  2. Division of Environmental Science, SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
  3. Department of Environmental Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
  4. Department of Sustainable Resources Management, SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
  5. SUNY College of Environmental Science and Forestry
  6. Department of Civil and Environmental Engineering, University of Delaware, Newark DE USA
  7. Microbiology Graduate Program, University of Delaware, Newark DE USA
  8. Sequencing and Genotyping Center, University of Delaware, Newark DE USA
  9. Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
These genome announcement narratives are associated with the manuscript "Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures" by Jennifer L. Goff, Chris Hahn, Rebecca A. Ingrassia, Chanistha Tiyapun, Gray G. Waldschmidt, Emma R. Smith, Miranda N. Marini, Olga Shevchenko, and Julia A. Maresca Assembeled genome sequences for all four genomes are available on this page and in the individual genome announcement narratives listed below. All methodological details can be found within the individual narratives.
Research Organization:
U.S. Department of Energy Systems Biology Knowledgebase
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI ID:
2345704
Country of Publication:
United States
Language:
English

References (25)

KBase: The United States Department of Energy Systems Biology Knowledgebase journal July 2018
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What is flux balance analysis? journal March 2010
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) journal November 2013
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PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies journal May 2012
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes journal February 2015
Efficiently gap-filling reaction networks journal June 2014
High-throughput generation, optimization and analysis of genome-scale metabolic models journal August 2010
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal May 2015
Translational recoding in archaea journal September 2012
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life journal August 2018
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree journal October 2010
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database journal November 2019
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
Identifying bacterial genes and endosymbiont DNA with Glimmer journal January 2007
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations journal January 2009
BLAT---The BLAST-Like Alignment Tool journal March 2002
Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism journal February 2006
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
The RAST Server: Rapid Annotations using Subsystems Technology journal January 2008
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments journal March 2010
FIGfams: yet another set of protein families journal September 2009
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM journal July 2013
Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks journal August 2008

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