eggNOG v4.0: nested orthology inference across 3686 organisms

Research output: Contribution to journalJournal articlepeer-review

Standard

eggNOG v4.0 : nested orthology inference across 3686 organisms. / Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian Milosz; Trachana, Kalliopi; Roth, Alexander; Huerta-Cepas, Jaime; Gabaldón, Toni; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars J; von Mering, Christian; Bork, Peer.

In: Nucleic Acids Research, Vol. 42, No. D1, 01.12.2013, p. D231-D239.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Powell, S, Forslund, K, Szklarczyk, DM, Trachana, K, Roth, A, Huerta-Cepas, J, Gabaldón, T, Rattei, T, Creevey, C, Kuhn, M, Jensen, LJ, von Mering, C & Bork, P 2013, 'eggNOG v4.0: nested orthology inference across 3686 organisms', Nucleic Acids Research, vol. 42, no. D1, pp. D231-D239. https://doi.org/10.1093/nar/gkt1253

APA

Powell, S., Forslund, K., Szklarczyk, D. M., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldón, T., Rattei, T., Creevey, C., Kuhn, M., Jensen, L. J., von Mering, C., & Bork, P. (2013). eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research, 42(D1), D231-D239. https://doi.org/10.1093/nar/gkt1253

Vancouver

Powell S, Forslund K, Szklarczyk DM, Trachana K, Roth A, Huerta-Cepas J et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research. 2013 Dec 1;42(D1):D231-D239. https://doi.org/10.1093/nar/gkt1253

Author

Powell, Sean ; Forslund, Kristoffer ; Szklarczyk, Damian Milosz ; Trachana, Kalliopi ; Roth, Alexander ; Huerta-Cepas, Jaime ; Gabaldón, Toni ; Rattei, Thomas ; Creevey, Chris ; Kuhn, Michael ; Jensen, Lars J ; von Mering, Christian ; Bork, Peer. / eggNOG v4.0 : nested orthology inference across 3686 organisms. In: Nucleic Acids Research. 2013 ; Vol. 42, No. D1. pp. D231-D239.

Bibtex

@article{4406cb4183c94e9abed3304427afaa69,
title = "eggNOG v4.0: nested orthology inference across 3686 organisms",
abstract = "With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.",
author = "Sean Powell and Kristoffer Forslund and Szklarczyk, {Damian Milosz} and Kalliopi Trachana and Alexander Roth and Jaime Huerta-Cepas and Toni Gabald{\'o}n and Thomas Rattei and Chris Creevey and Michael Kuhn and Jensen, {Lars J} and {von Mering}, Christian and Peer Bork",
year = "2013",
month = dec,
day = "1",
doi = "10.1093/nar/gkt1253",
language = "English",
volume = "42",
pages = "D231--D239",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "D1",

}

RIS

TY - JOUR

T1 - eggNOG v4.0

T2 - nested orthology inference across 3686 organisms

AU - Powell, Sean

AU - Forslund, Kristoffer

AU - Szklarczyk, Damian Milosz

AU - Trachana, Kalliopi

AU - Roth, Alexander

AU - Huerta-Cepas, Jaime

AU - Gabaldón, Toni

AU - Rattei, Thomas

AU - Creevey, Chris

AU - Kuhn, Michael

AU - Jensen, Lars J

AU - von Mering, Christian

AU - Bork, Peer

PY - 2013/12/1

Y1 - 2013/12/1

N2 - With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.

AB - With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.

U2 - 10.1093/nar/gkt1253

DO - 10.1093/nar/gkt1253

M3 - Journal article

C2 - 24297252

VL - 42

SP - D231-D239

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -

ID: 91131868