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KBase Narrative - kb_DRAM P. normanii annotation with model

Dataset ·
 [1];  [2]
  1. Colorado State University Fort Collins; Lawrence Berkeley National Laboratory (LBNL)
  2. Argonne National Laboratory ANL
Here we are annotating a P. normanii metagenome assembled genome using both DRAM and RAST then using those annotations to build models. The genome is from NCBI genome ID GCA_000398025.1
Research Organization:
U.S. Department of Energy Systems Biology Knowledgebase
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
DOE Contract Number:
SC0019746; SC0021350
OSTI ID:
1893104
Country of Publication:
United States
Language:
English

References (19)

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
The RAST Server: Rapid Annotations using Subsystems Technology journal January 2008
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) journal November 2013
‘Unknown’ proteins and ‘orphan’ enzymes: the missing half of the engineering parts list – and how to find it journal December 2009
Efficiently gap-filling reaction networks journal June 2014
Identification, variation and transcription of pneumococcal repeat sequences journal February 2011
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies journal May 2012
BLAT---The BLAST-Like Alignment Tool journal March 2002
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
Insights from 20 years of bacterial genome sequencing journal February 2015
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes journal February 2015
High-throughput generation, optimization and analysis of genome-scale metabolic models journal August 2010
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM journal July 2013
Translational recoding in archaea journal September 2012
FIGfams: yet another set of protein families journal September 2009
Annotation and curation of uncharacterized proteins- challenges journal March 2015
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes journal November 2020
Combining multiple functional annotation tools increases coverage of metabolic annotation journal December 2018

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