Filters








18 Hits in 2.7 sec

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork
2016 Nucleic Acids Research  
It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades.  ...  Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic  ...  D.R.M. would further like to thank Sebastian Schmidt and Frank Aylward for helpful discussions.  ... 
doi:10.1093/nar/gkw989 pmid:28053165 pmcid:PMC5210662 fatcat:xg2rdi5xpvdzzipjnyuhulrdry

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

2019 Nucleic Acids Research  
Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain.  ...  Microbiology depends on the availability of annotated microbial genomes for many applications.  ...  ACKNOWLEDGEMENTS The authors would like to thank the members of the Bork group, in particular Yan-Ping Yuan for technical support.  ... 
doi:10.1093/nar/gkz1002 pmid:31647096 pmcid:PMC7145564 fatcat:hqvc3agp5rarlcwm62ekvrkzta

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, Christian von Mering, Peer Bork
2018 Nucleic Acids Research  
eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations.  ...  Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets.  ...  Version 5 of eggNOG should thus be a useful resource for ecological, evolutionary or medical -omics analysis, also serving as an entry point for fast functional annotation of newly sequenced genes, genomes  ... 
doi:10.1093/nar/gky1085 pmid:30418610 fatcat:7gq2yqm3hjgspetm2c36xd3c3u

GUNC: detection of chimerism and contamination in prokaryotic genomes

Askarbek Orakov, Anthony Fullam, Luis Pedro Coelho, Supriya Khedkar, Damian Szklarczyk, Daniel R. Mende, Thomas S. B. Schmidt, Peer Bork
2021 Genome Biology  
GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality.  ...  We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome's full complement of genes  ...  We thank Oleksandr M Maistrenko and Donovan Parks for comments and feedback on the manuscript, as well as all members of the Bork lab for insightful discussions.  ... 
doi:10.1186/s13059-021-02393-0 pmid:34120611 pmcid:PMC8201837 fatcat:j4iim444rbal3iwbvevbol4gyi

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity [article]

Oleksandr M. Maistrenko, Daniel R. Mende, Mechthild Luetge, Falk Hildebrand, Thomas SB Schmidt, Simone S. Li, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
2019 bioRxiv   pre-print
Hence, pan-genomes are increasingly used to characterize the strain diversity of prokaryotic species.  ...  We show that many pan-genome features such as functional diversity and core genome nucleotide diversity are correlated to each other.  ...  Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, et al. proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.  ... 
doi:10.1101/735696 fatcat:454jtye3nneojd65wccn7dk6fq

MVP: a microbe–phage interaction database

Na L Gao, Chengwei Zhang, Zhanbing Zhang, Songnian Hu, Martin J Lercher, Xing-Ming Zhao, Peer Bork, Zhi Liu, Wei-Hua Chen
2017 Nucleic Acids Research  
from published datasets, public databases and re-analysis of genomic and metagenomic sequences.  ...  The main purpose of MVP (Microbe Versus Phage) is to provide a comprehensive catalog of phage-microbe interactions and assist users to select phage(s) that can target (and potentially to manipulate) specific  ...  Second, we identified putative prophage sequences from complete bacterial and archaeal genomes downloaded from the NCBI prokaryotic reference genome database (40) and EMBL proGenomes database (41) .  ... 
doi:10.1093/nar/gkx1124 pmid:29177508 pmcid:PMC5753265 fatcat:jhblq52svjbjngnmapzsuhlpfy

Metagenomics: a path to understanding the gut microbiome

Sandi Yen, Jethro S. Johnson
2021 Mammalian Genome  
AbstractThe gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level.  ...  Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded  ...  One of the largest resources for metagenome annotation and functional interpretation is the Kyoto Encyclopaedia of Genes and Genomes (KEGG), which curates functional information at both a genomic and systems  ... 
doi:10.1007/s00335-021-09889-x pmid:34259891 pmcid:PMC8295064 fatcat:a7pfj4ugfzfh5nzyybpzko25eu

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives

Luca Ambrosino, Michael Tangherlini, Chiara Colantuono, Alfonso Esposito, Mara Sangiovanni, Marco Miralto, Clementina Sansone, Maria Luisa Chiusano
2019 Marine Drugs  
As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies  ...  It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment  ...  The proGenomes initiative represents an attempt to provide a highly accurate prokaryotic genome database with curated taxonomic affiliations and functional annotations based on different collections, including  ... 
doi:10.3390/md17100576 pmid:31614509 pmcid:PMC6835618 fatcat:jch7dwrhgrhipihvf42zr6bljm

GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes [article]

Askarbek Orakov, Anthony Fullam, Luis Pedro Coelho, Supriya Khedkar, Damian Szklarczyk, Daniel R Mende, Thomas SB Schmidt, Peer Bork
2020 biorxiv/medrxiv   pre-print
We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome's full complement of genes  ...  GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality. Source code (GPLv3+): https://github.com/grp-bork/gunc  ...  We thank Oleksandr M Maistrenko for comments and feedback on the manuscript, as well as all members of the Bork lab for insightful discussions. Author Contributions  ... 
doi:10.1101/2020.12.16.422776 fatcat:wgkb3bprvja65mkhoasodpdyjm

Nitrogen availability drives gene length of dominant prokaryotes and diversity of genes acquiring Nitrogen-species in oceanic systems [article]

Leon Dlugosch, Anja Poehlein, Bernd Wemheuer, Birgit Pfeiffer, Helge Ansgar Giebel, Rolf Daniel, Meinhard Simon
2021 bioRxiv   pre-print
Our findings introduce a novel and most effective mode of evolutionary adaptation of prokaryotes to save resources including N and energy.  ...  Nitrogen (N) is a key element for prokaryotes in the oceans and often limits phytoplankton primary production.  ...  In total 38% percent of nr genes were functionally annotated by homology to 92 a KEGG ortholog (KO) .  ... 
doi:10.1101/2021.01.10.426031 fatcat:zxckag3bancfvlah5virwemsma

Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile

Daniel Kurth, Dario Elias, María Cecilia Rasuk, Manuel Contreras, María Eugenia Farías, Andrea Franzetti
2021 PLoS ONE  
Regardless of the differences at the taxonomic level, functionally the two mats were similar. Thus, similar roles could be fulfilled by different organisms.  ...  In spite of presenting less taxonomic diversity, Tebenquiche mats showed increased abundance and variety of rhodopsin genes.  ...  Acknowledgments The authors thank Marco Contreras for his support during the sampling campaign and Geol.  ... 
doi:10.1371/journal.pone.0246656 pmid:33561170 fatcat:ijd2d2bpgff7tbdqatdir6visa

Dispersal strategies shape persistence and evolution of human gut bacteria

Falk Hildebrand, Toni I. Gossmann, Clémence Frioux, Ezgi Özkurt, Pernille Neve Myers, Pamela Ferretti, Michael Kuhn, Mohammad Bahram, Henrik Bjørn Nielsen, Peer Bork
2021 Cell Host and Microbe  
Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota.  ...  Human gut bacterial strains can co-exist with their hosts for decades, but little is known about how these microbes persist and disperse, and evolve thereby.  ...  ., and Bork, P. (2017). proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. Nucleic Acids Res 45, D529-D534.  ... 
doi:10.1016/j.chom.2021.05.008 pmid:34111423 pmcid:PMC8288446 fatcat:4h5p2eyjpjditbrtoowjv2toly

Structure and function of the global topsoil microbiome

Mohammad Bahram, Falk Hildebrand, Sofia K. Forslund, Jennifer L. Anderson, Nadejda A. Soudzilovskaia, Peter M. Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H. Medema (+9 others)
2018 Nature  
Dutch law entitles the maker of a short scientific work funded either wholly or partially by Dutch public funds to make that work publicly available for no consideration following a reasonable period of  ...  You are permitted to download and use the publication for personal purposes. All rights remain with the author(s) and/or copyrights owner(s) of this work.  ...  Liiv for technical and laboratory assistance; S. Waszak for comments on the manuscript; Y. P. Yuan and A. Glazek for bioinformatics support and A.  ... 
doi:10.1038/s41586-018-0386-6 pmid:30069051 fatcat:t4c25q37wnhs5owamf4deytm3i

Discovery, diversity and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts [article]

Anastasia Gulyaeva, Sanzhima Garmaeva, Renate A.A.A. Ruigrok, Daoming Wang, Niels P. Riksen, Mihai G. Netea, Cisca Wijmenga, Rinse K. Weersma, Jingyuan Fu, Arnau Vich Vila, Alexander Kurilshikov, Alexandra Zhernakova
2021 bioRxiv   pre-print
Analysis of their genomic features revealed that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination.  ...  Finally, we explored the temporal stability of crAss-like phages over a 4-year period and identified associations between the abundance of crAss-like phages and several human phenotypes, including depletion  ...  We would like to thank Lianmin Chen and Sergio Andreu-Sánchez for technical support, Kate Mc Intyre for editing the manuscript, the Center for Information Technology of the University of Groningen for  ... 
doi:10.1101/2021.06.01.446427 fatcat:hbcajzqwynadllkzsv5jcmilby

Co-culture and biogeography of Prochlorococcus and SAR11 [article]

Jamie W Becker, Shane L Hogle, Kali Rosendo, Sallie W Chisholm
2018 bioRxiv   pre-print
To place our results in context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes.  ...  With a combined global population of about 2.7 x 1028 cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro.  ...  Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, et al. 563 proGenomes: a resource for consistent functional and taxonomic annotations of 564 prokaryotic genomes.  ... 
doi:10.1101/460428 fatcat:lsiw44qxqbaltko4or6tincxsu
« Previous Showing results 1 — 15 out of 18 results