eggNOG v4.0: nested orthology inference across 3686 organisms (Q30002339)

11

0 references

Peer Bork

13

0 references

Damian Szklarczyk

3

0 references

Jaime Huerta-Cepas

6

0 references

Christian von Mering

12

0 references

Toni Gabaldón

7

0 references

Sofia K. Forslund

2

0 references

Sean T Powell

Sean Powell

1

0 references

Christopher J. Creevey

Chris Creevey

9

0 references

Thomas Rattei

Thomas Rattei

8

0 references

Kalliopi Trachana

4

Kalliopi Trachana

0 references

author name string

Alexander Roth

5

0 references

Michael Kuhn

Creative Commons Attribution-NonCommercial 3.0 Unported

10

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language of work or name

English

0 references

publication date

1 December 2013

0 references

published in

Nucleic Acids Research

0 references

volume

42

0 references

page(s)

D231-D239

0 references

issue

D1

0 references

copyright license

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Update on activities at the Universal Protein Resource (UniProt) in 2013

22 May 2017

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The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

22 May 2017

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The Pfam protein families database

22 May 2017

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NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

22 May 2017

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22 May 2017

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SMART 7: recent updates to the protein domain annotation resource

22 May 2017

1 reference

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Accelerated Profile HMM Searches

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Orthology prediction methods: a quality assessment using curated protein families

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

22 May 2017

1 reference

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Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

22 May 2017

1 reference

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OMA 2011: orthology inference among 1000 complete genomes

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

22 May 2017

1 reference

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The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

22 May 2017

1 reference

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A new generation of homology search tools based on probabilistic inference

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

2x genomes--depth does matter

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Database resources of the National Center for Biotechnology Information

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

eggNOG: automated construction and annotation of orthologous groups of genes

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

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

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

M-Coffee: combining multiple sequence alignment methods with T-Coffee

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Orthologs, paralogs, and evolutionary genomics

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Phylogenomics and the reconstruction of the tree of life

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

The COG database: an updated version includes eukaryotes

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Gene ontology: tool for the unification of biology

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

A genomic perspective on protein families

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Analysis of compositionally biased regions in sequence databases

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Distinguishing Homologous from Analogous Proteins

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Basic local alignment search tool

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Rapid and sensitive sequence comparison with FASTP and FASTA

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Metagenomic species profiling using universal phylogenetic marker genes

22 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Genomic variation landscape of the human gut microbiome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Identifying single copy orthologs in Metazoa

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

New approaches for isolation of previously uncultivated oral bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Evaluating ortholog prediction algorithms in a yeast model clade

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Limitations of next-generation genome sequence assembly

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Phylogenetic and functional assessment of orthologs inference projects and methods

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Assessing performance of orthology detection strategies applied to eukaryotic genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Benchmarking ortholog identification methods using functional genomics data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Protein database searches using compositionally adjusted substitution matrices

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

The impact of comparative genomics on our understanding of evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Orthologs, paralogs and genome comparisons

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Sensitivity and selectivity in protein similarity searches: a comparison of Smith-Waterman in hardware to BLAST and FASTA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Maximum discrimination hidden Markov models of sequence consensus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Functional and evolutionary implications of gene orthology.

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1253

Accurate and universal delineation of prokaryotic species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1253

Dissecting plant genomes with the PLAZA comparative genomics platform

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1253

Genome-wide experimental determination of barriers to horizontal gene transfer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1253

Does a tree-like phylogeny only exist at the tips in the prokaryotes?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1253

Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1253

Benchmarking homology detection procedures with low complexity filters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT1253

Using the KEGG database resource.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3964997

Modules, multidomain proteins and organismic complexity

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24297252

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKT1253

1 reference

journals/nar/PowellFST0HGRCKJMB14

171082

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

171082

1 reference

1 reference

1 reference