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eggNOG v4.0: nested orthology inference across 3686 organisms
2013
Nucleic Acids Research
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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 ...
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 ...
., D.S. and A.R. generated the orthologous groups. K.F. and D.S. determined clades and performed the functional annotation. J.H. and T.G. created the alignments and ...
doi:10.1093/nar/gkt1253
pmid:24297252
pmcid:PMC3964997
fatcat:tppseymmmbhb5ndnyxnwoktcbq
Comparative transcriptome reveals the potential modulation mechanisms of estradiol affecting ovarian development of female Portunus trituberculatus
2019
PLoS ONE
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This study performed transcriptome sequencing of ovary, hepatopancreas, brain ganglion, eyestalk, and mandibular organ of crabs after estradiol treatment (0.1μg g-1 crab weight). ...
A total of 23, 806 genes were annotated, and 316, 1300, 669, 142, 383 genes were expressed differently in ovary, hepatopancreas, brain ganglion, eyestalk, and mandibular organ respectively. ...
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. eggNOG v4.0: nested orthology inference across 3686 organisms. ...
doi:10.1371/journal.pone.0226698
pmid:31856263
pmcid:PMC6922394
fatcat:u7b6lr4ttbe47juzbgxlkji4te
Function and functional redundancy in microbial systems
2018
Nature Ecology & Evolution
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result from ecological drift between equivalent organisms. ...
On the other hand, the identity of taxa encoding each function 6 can vary substantially across space or time with little effect on the function, and this taxonomic variability 7 is frequently thought to ...
Powell, S. et al. eggnog v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 331 42, D231-D239 (2014).332 [4] O'Leary, N.A. et al. ...
doi:10.1038/s41559-018-0519-1
pmid:29662222
fatcat:porwxpryzzegbfin4t4trqbfuq
Transcriptome Analysis of Taxillusi chinensis (DC.) Danser Seeds in Response to Water Loss
2017
PLoS ONE
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Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. eggNOG v4.0: nested orthology inference across 3686 organisms. ...
Then, likely proteins encoded by the assembled transcripts were mapped to eggNOG database and proteins encoded by 24,580 (14.94%) transcripts were distributed in EuKaryotic Orthologous Groups (KOG), Clusters ...
doi:10.1371/journal.pone.0169177
pmid:28046012
pmcid:PMC5207531
fatcat:cs7nxdqqrjboznxecbhunklp2i
Dispersal strategies shape persistence and evolution of human gut bacteria
2021
Cell Host and Microbe
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Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldó n, T., Rattei, T., Creevey, C., Kuhn, M., et al. (2014). eggNOG v4.0: nested orthology inference across 3686 ...
EggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47, D309-D314. ...
doi:10.1016/j.chom.2021.05.008
pmid:34111423
pmcid:PMC8288446
fatcat:4h5p2eyjpjditbrtoowjv2toly
New insight into the gut microbiome through metagenomics
2015
Advances in Genomics and Genetics
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Powell S, Forslund K, Szklarczyk D, et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res . 2014;42(D1):D231–D239.
51. ...
Numerous databases and online tools, such as KEGG, 49the Clusters Of Orthologous Groups database (COG), 60Pfam, 61SEED, 62eggNOG, 50MG-RAST, 63CAMERA, 64and IMG/M, 65can be used to infer the functional ...
doaj:becf1dc1b606466d80e46ea29725f989
fatcat:y4uqfliamzd6lbigojimkyksua
Metaepigenomic analysis reveals the unexplored diversity of DNA methylations in an environmental prokaryotic community
[article]
2018
bioRxiv
pre-print
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EggNOG v4.0: Nested orthology inference across 3686 organisms. Nucleic Acids Res. 509 42, D231-D239 (2014). 510 44. UniProt Consortium. ...
This high ratio of methylation-lacking 351 organisms contrasts remarkably with a previous report in which prokaryotic genomes were found to rarely 352 lack DNA methylation systems (<7%) 13 . ...
doi:10.1101/380360
fatcat:mucvb47flfc7xlyrw32uirwjqy
A study of protein coding genes in Enterobacteriaceae family: essentiality of genes and orthology
[article]
2018
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We introduce an ortholog clustering algorithm that can be used to nd orthologous genes to help with annotating genomes, as well as nding the evolutionary relationships between them. ...
J., von Mering, C., and Bork, P. (2014). eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research, 42(Database issue):D231-D239. [Pruitt et al., 2007] Pruitt, K. ...
High-throughput studies infer information about organisms from pools of biological molecules such as DNA, RNA, protein or metabolites. ...
doi:10.26021/7562
fatcat:hbqvdo2kwvbwphum3t37xfwkzm
Metabolic and genomic profiling of actinobacteria strains : from new natural products to biosynthetic pathways
[article]
2019
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Powell, S. et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research 42, 231-239 (2014). 30. Liu, Q. et al. ...
The organization of the alp gene cluster lacks the co-linearity due to its unusual domain orders and domains acting across modules, which is a well-known feature of trans-AT-PKSs . ...
doi:10.22028/d291-27785
fatcat:vwqkllwanbd4jjhgztagrxefqu