Annotation error in public databases: misannotation of molecular function in enzyme superfamilies (Q21145347)

18 August 2022

3

Igor

Dodevski

Igor Dodevski

1 reference

18 August 2022

1

Alexandra M

Schnoes

Alexandra M Schnoes

1 reference

18 August 2022

Shoshana D Brown

2

Shoshana D

Brown

1 reference

20011109

PLOS Computational Biology

18 August 2022

language of work or name

English

0 references

publication date

December 2009

0 references

published in

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volume

5

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issue

12

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page(s)

e1000605

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copyright license

Creative Commons Attribution 4.0 International

start time

11 December 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

2 references

Europe PubMed Central

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A gold standard set of mechanistically diverse enzyme superfamilies

19 March 2017

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19 March 2017

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19 March 2017

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19 March 2017

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Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies

19 March 2017

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19 March 2017

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19 March 2017

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Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach

19 March 2017

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Detecting protein function and protein-protein interactions from genome sequences

6 April 2017

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Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

7 April 2017

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7 April 2017

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Conservation of gene order: a fingerprint of proteins that physically interact

7 April 2017

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Quantitative assessment of protein function prediction from metagenomics shotgun sequences

7 April 2017

1 reference

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Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

10 May 2017

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Protein function prediction--the power of multiplicity

10 May 2017

1 reference

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Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2781113

Annotating proteins with generalized functional linkages

12 September 2017

1 reference

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Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation

12 September 2017

1 reference

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The Mouse Genome Database (MGD): mouse biology and model systems

12 September 2017

1 reference

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Predicting protein function from sequence and structure

12 September 2017

1 reference

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Multidimensional annotation of the Escherichia coli K-12 genome

12 September 2017

1 reference

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Novel hopanoid cyclases from the environment

12 September 2017

1 reference

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Protein annotation at genomic scale: the current status

12 September 2017

1 reference

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Manual curation is not sufficient for annotation of genomic databases

12 September 2017

1 reference

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Protein function space: viewing the limits or limited by our view?

12 September 2017

1 reference

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Estimating the annotation error rate of curated GO database sequence annotations

12 September 2017

1 reference

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Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database

12 September 2017

1 reference

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SCOPEC: a database of protein catalytic domains.

12 September 2017

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12 September 2017

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12 September 2017

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Enzyme function less conserved than anticipated.

12 September 2017

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Intrinsic errors in genome annotation

12 September 2017

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Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption.

12 September 2017

1 reference

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Evolution of function in protein superfamilies, from a structural perspective.

12 September 2017

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Cloning and characterization of glyoxalase I from soybean

12 September 2017

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Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily

12 September 2017

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Go hunting in sequence databases but watch out for the traps

30 May 2018

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Ig-like domains on bacteriophages: a tale of promiscuity and deceit

30 May 2018

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21 January 2018

Errors in Genome Reviews

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Whole-genome sequence annotation: 'Going wrong with confidence'.

21 January 2018

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21 January 2018

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Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily

21 January 2018

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How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?

21 January 2018

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DNA data. Proposal to 'Wikify' GenBank meets stiff resistance

21 January 2018

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21 January 2018

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Representing structure-function relationships in mechanistically diverse enzyme superfamilies.

21 January 2018

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29 November 2018

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Modeling the percolation of annotation errors in a database of protein sequences

21 January 2018

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12 December 2020

Errors in genome annotation

1 reference

12 December 2020

What we do not know about sequence analysis and sequence databases

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12 December 2020

Percolation of annotation errors through hierarchically structured protein sequence databases

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12 December 2020

10.1371/JOURNAL.PCBI.1000605

Identifiers

DOI

1 reference

journals/ploscb/SchnoesBDB09

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_urwda7nh5zeb7ehbm7puqe54aa

28 January 2021

Fatcat ID

0 references

1 reference

1 reference

20011109

1 reference