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Title: Enabling comparative modeling of closely related genomes: Example genus Brucella

Journal Article · · 3 Biotech
 [1];  [2];  [2];  [3];  [4];  [2];  [3];  [5];  [4];  [6];  [5];  [6]
  1. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Minho, Braga (Portugal)
  2. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
  3. Argonne National Lab. (ANL), Argonne, IL (United States)
  4. Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
  5. Argonne National Lab. (ANL), Argonne, IL (United States); Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
  6. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
+ Show Author Affiliations

For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this study, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of metabolic models on closely related genomes, using fifteen strains of genus Brucella, which contains pathogens of both humans and livestock. This study lead to the identification and subsequent correction of inconsistent annotations in the SEED database, as well as the identification of 31 biochemical reactions that are common to Brucella, which are not originally identified by automated metabolic reconstructions. We are currently implementing this protocol for improving automated annotations within the SEED database and these improvements have been propagated into PATRIC, Model-SEED, KBase and RAST. This method is an enabling step for the future creation of consistent annotation systems and high-quality model reconstructions that will support in predicting accurate phenotypes such as pathogenicity, media requirements or type of respiration.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1222724
Journal Information:
3 Biotech, Vol. 5, Issue 1; ISSN 2190-572X
Publisher:
SpringerCopyright Statement
Country of Publication:
United States
Language:
English

References (30)

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High-throughput generation, optimization and analysis of genome-scale metabolic models journal August 2010
A protocol for generating a high-quality genome-scale metabolic reconstruction journal January 2010
The use of gene clusters to infer functional coupling journal March 1999
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 journal January 2003
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The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes journal September 2005
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Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model journal October 2012
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Genome update: the 1000th genome - a cautionary tale journal January 2010
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Cited By (2)

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database journal February 2016
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database journal February 2016

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