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In search of genome annotation consistency: solid gene clusters and how to use them

Journal Article · · 3 Biotech
 [1];  [2];  [3];  [4];  [5]
  1. Univ. of Illinois at Urbana-Champaign, IL (United States). Inst. for Genomic Biology; OSTI
  2. Univ. of Illinois at Urbana-Champaign, IL (United States). Inst. for Genomic Biology; Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Microbiology
  3. Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science
  4. Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
  5. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science
+ Show Author Affiliations
Maintaining consistency in genome annotations is important for supporting many computational tasks, particularly metabolic modeling. The SEED project has implemented a process that improves annotation consistencies across microbial genomes for proteins with conserved sequences and genomic context. In this research report, we describe this process and show how this effort has resulted in improvements to microbial genome annotations in the SEED. We also compare SEED annotation consistencies with other commonly used resources such as IMG (the Joint Genome Institute’s Integrated Microbial Genomes system), RefSeq (the National Center for Biotechnology Information’s Reference Sequence Database), Swiss-Prot (the annotated protein sequence database of the Swiss Institute of Bioinformatics, European Molecular Biology Laboratory and the European Bioinformatics Institute) and TrEMBL (Translated European Molecular Biology Laboratory nucleotide sequence data Library). Our analysis indicates that manual and computational efforts are paying off for the databases where consistency is a major goal.
Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1815515
Journal Information:
3 Biotech, Journal Name: 3 Biotech Journal Issue: 3 Vol. 4; ISSN 2190-572X
Publisher:
SpringerCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (3)

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database journal February 2016
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes journal February 2015
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) journal November 2013

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Automatic annotation
Protein clusters