(Q38508638)

3 September 2017

A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions (English)

1 reference

protein function prediction

3 September 2017

0 references

0 references

3

Eugene Kolker

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author name string

Brenton Louie

series ordinal

1

1 reference

PMCID

2760442

3 September 2017

Roger Higdon

series ordinal

2

1 reference

PMCID

2760442

3 September 2017

language of work or name

English

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publication date

21 October 2009

1 reference

3 September 2017

1 reference

3 September 2017

4

1 reference

3 September 2017

e7546

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3 September 2017

10

1 reference

Creative Commons Attribution 4.0 International

3 September 2017

start time

21 October 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Validating annotations for uncharacterized proteins in Shewanella oneidensis

6 September 2017

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Annotation-based inference of transporter function

6 September 2017

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Metrics for GO based protein semantic similarity: a systematic evaluation

6 September 2017

1 reference

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Quantitative sequence-function relationships in proteins based on gene ontology

6 September 2017

1 reference

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Protein annotation at genomic scale: the current status

6 September 2017

1 reference

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Quantitative assessment of relationship between sequence similarity and function similarity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Estimating the annotation error rate of curated GO database sequence annotations

6 September 2017

1 reference

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NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

6 September 2017

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New metrics for comparative genomics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

BLAST: improvements for better sequence analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Automatic annotation of protein function

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations

6 September 2017

1 reference

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Entrez Gene: gene-centered information at NCBI

6 September 2017

1 reference

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GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes

6 September 2017

1 reference

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'Conserved hypothetical' proteins: prioritization of targets for experimental study

6 September 2017

1 reference

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BLAST: at the core of a powerful and diverse set of sequence analysis tools

6 September 2017

1 reference

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Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Identifying protein function--a call for community action

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Evaluation of annotation strategies using an entire genome sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

The past, present and future of genome-wide re-annotation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Intrinsic errors in genome annotation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Database verification studies of SWISS-PROT and GenBank

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Gene ontology: tool for the unification of biology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Powers and pitfalls in sequence analysis: the 70% hurdle

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Twilight zone of protein sequence alignments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Protein family classification based on searching a database of blocks

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Identification of common molecular subsequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Annotation transfer for genomics: measuring functional divergence in multi-domain proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Functional and structural genomics using PEDANT.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2760442

Errors in genome annotation

31 August 2018

1 reference

12 December 2020

What we do not know about sequence analysis and sequence databases

1 reference

12 December 2020

Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequence

1 reference

12 December 2020

Practical limits of function prediction

1 reference

12 December 2020

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

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0007546

Identifiers

DOI

1 reference

3 September 2017

0 references

1 reference

3 September 2017

1 reference

PMCID

2760442