A fast comparative genome browser for diverse bacteria and archaea

Price, Morgan N.; Arkin, Adam P.; Promponas, ed., Vasilis J.

doi:10.1371/journal.pone.0301871

A fast comparative genome browser for diverse bacteria and archaea

Journal Article · Tue Apr 09 00:00:00 EDT 2024 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0301871· OSTI ID:2335832

; Arkin, Adam P.; Promponas, ed., Vasilis J.

Genome sequencing has revealed an incredible diversity of bacteria and archaea, but there are no fast and convenient tools for browsing across these genomes. It is cumbersome to view the prevalence of homologs for a protein of interest, or the gene neighborhoods of those homologs, across the diversity of the prokaryotes. We developed a web-based tool, fast . genomics , that uses two strategies to support fast browsing across the diversity of prokaryotes. First, the database of genomes is split up. The main database contains one representative from each of the 6,377 genera that have a high-quality genome, and additional databases for each taxonomic order contain up to 10 representatives of each species. Second, homologs of proteins of interest are identified quickly by using accelerated searches, usually in a few seconds. Once homologs are identified, fast . genomics can quickly show their prevalence across taxa, view their neighboring genes, or compare the prevalence of two different proteins. Fast . genomics is available at https://fast.genomics.lbl.gov .

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2335832

Alternate ID(s):: OSTI ID: 2448507

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 4 Vol. 19; ISSN 1932-6203

Publisher:: Public Library of Science (PLoS)Copyright Statement

Country of Publication:: United States

Language:: English

References (45)

Conservation of gene order: a fingerprint of proteins that physically interact Dandekar, T. Trends in Biochemical Sciences, Vol. 23, Issue 9 https://doi.org/10.1016/S0968-0004(98)01274-2	journal	September 1998
Lateral gene transfer Zhaxybayeva, Olga; Doolittle, W. Ford Current Biology, Vol. 21, Issue 7 https://doi.org/10.1016/j.cub.2011.01.045	journal	April 2011
EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools Oberg, Nils; Zallot, Rémi; Gerlt, John A. Journal of Molecular Biology, Vol. 435, Issue 14 https://doi.org/10.1016/j.jmb.2023.168018	journal	July 2023
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas Nature Biotechnology, Vol. 35, Issue 8 https://doi.org/10.1038/nbt.3893	journal	August 2017
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets Steinegger, Martin; Söding, Johannes Nature Biotechnology, Vol. 35, Issue 11 https://doi.org/10.1038/nbt.3988	journal	October 2017
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life Parks, Donovan H.; Chuvochina, Maria; Waite, David W. Nature Biotechnology, Vol. 36, Issue 10 https://doi.org/10.1038/nbt.4229	journal	August 2018
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles Pellegrini, M.; Marcotte, E. M.; Thompson, M. J. Proceedings of the National Academy of Sciences, Vol. 96, Issue 8 https://doi.org/10.1073/pnas.96.8.4285	journal	April 1999
A powerful non-homology method for the prediction of operons in prokaryotes Moreno-Hagelsieb, G.; Collado-Vides, J. Bioinformatics, Vol. 18, Issue Suppl 1 https://doi.org/10.1093/bioinformatics/18.suppl_1.S329	journal	July 2002
PhyloCorrelate: inferring bacterial gene–gene functional associations through large-scale phylogenetic profiling Tremblay, Benjamin J. -M; Lobb, Briallen; Doxey, Andrew C. Bioinformatics, Vol. 37, Issue 1 https://doi.org/10.1093/bioinformatics/btaa1105	journal	January 2021
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation Saha, Chayan Kumar; Sanches Pires, Rodrigo; Brolin, Harald Bioinformatics, Vol. 37, Issue 9 https://doi.org/10.1093/bioinformatics/btaa788	journal	December 2020
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions Yu, Yi-Kuo; Altschul, Stephen F. Bioinformatics, Vol. 21, Issue 7 https://doi.org/10.1093/bioinformatics/bti070	journal	October 2004
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
CD-HIT: accelerated for clustering the next-generation sequencing data Fu, Limin; Niu, Beifang; Zhu, Zhengwei Bioinformatics, Vol. 28, Issue 23 https://doi.org/10.1093/bioinformatics/bts565	journal	October 2012
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale Cantalapiedra, Carlos P.; Hernández-Plaza, Ana; Letunic, Ivica Molecular Biology and Evolution, Vol. 38, Issue 12 https://doi.org/10.1093/molbev/msab293	journal	October 2021
Inference and Analysis of the Relative Stability of Bacterial Chromosomes Rocha, Eduardo P. C. Molecular Biology and Evolution, Vol. 23, Issue 3 https://doi.org/10.1093/molbev/msj052	journal	November 2005
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models Varadi, Mihaly; Anyango, Stephen; Deshpande, Mandar Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1061	journal	November 2021
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest Szklarczyk, Damian; Kirsch, Rebecca; Koutrouli, Mikaela Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1000	journal	November 2022
eggNOG 6.0: enabling comparative genomics across 12 535 organisms Hernández-Plaza, Ana; Szklarczyk, Damian; Botas, Jorge Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1022	journal	November 2022
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes Fullam, Anthony; Letunic, Ivica; Schmidt, Thomas S. B. Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1078	journal	November 2022
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective Botas, Jorge; Rodríguez del Río, Álvaro; Giner-Lamia, Joaquín Nucleic Acids Research, Vol. 50, Issue W1 https://doi.org/10.1093/nar/gkac367	journal	May 2022
The IMG/M data management and analysis system v.7: content updates and new features Chen, I-Min A.; Chu, Ken; Palaniappan, Krishnaveni Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac976	journal	November 2022
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
A novel method for accurate operon predictions in all sequenced prokaryotes Price, M. N. Nucleic Acids Research, Vol. 33, Issue 3 https://doi.org/10.1093/nar/gki232	journal	February 2005
STRING 7--recent developments in the integration and prediction of protein interactions von Mering, C.; Jensen, L. J.; Kuhn, M. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl825	journal	January 2007
MicrobesOnline: an integrated portal for comparative and functional genomics Dehal, P. S.; Joachimiak, M. P.; Price, M. N. Nucleic Acids Research, Vol. 38, Issue suppl_1, p. D396-D400 https://doi.org/10.1093/nar/gkp919	journal	November 2009
TIGRFAMs and Genome Properties in 2013 Haft, Daniel H.; Selengut, Jeremy D.; Richter, Roland A. Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1234	journal	November 2012
Pfam: the protein families database Finn, Robert D.; Bateman, Alex; Clements, Jody Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1223	journal	November 2013
CDD: NCBI's conserved domain database Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1221	journal	November 2014
Expanded microbial genome coverage and improved protein family annotation in the COG database Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1223	journal	November 2014
SANSparallel: interactive homology search against Uniprot Somervuo, Panu; Holm, Liisa Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv317	journal	April 2015
InterPro in 2017—beyond protein family and domain annotations Finn, Robert D.; Attwood, Teresa K.; Babbitt, Patricia C. Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1107	journal	November 2016
HMMER web server: 2018 update Potter, Simon C.; Luciani, Aurélien; Eddy, Sean R. Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky448	journal	June 2018
AnnoTree: visualization and exploration of a functionally annotated microbial tree of life Mendler, Kerrin; Chen, Han; Parks, Donovan H. Nucleic Acids Research, Vol. 47, Issue 9 https://doi.org/10.1093/nar/gkz246	journal	April 2019
Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences Huynen, M. Genome Research, Vol. 10, Issue 8 https://doi.org/10.1101/gr.10.8.1204	journal	August 2000
Adaptive seeds tame genomic sequence comparison Kielbasa, S. M.; Wan, R.; Sato, K. Genome Research, Vol. 21, Issue 3 https://doi.org/10.1101/gr.113985.110	journal	January 2011
Genome Alignment, Evolution of Prokaryotic Genome Organization, and Prediction of Gene Function Using Genomic Context Wolf, Yuri I.; Rogozin, Igor B.; Kondrashov, Alexey S. Genome Research, Vol. 11, Issue 3 https://doi.org/10.1101/gr.161901	journal	February 2001
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Curated BLAST for Genomes Price, Morgan N.; Arkin, Adam P. mSystems, Vol. 4, Issue 2 https://doi.org/10.1128/mSystems.00072-19	journal	March 2019
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process Basu, Malay K.; Selengut, Jeremy D.; Haft, Daniel H. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-434	journal	November 2011
New finite-size correction for local alignment score distributions Park, Yonil; Sheetlin, Sergey; Ma, Ning BMC Research Notes, Vol. 5, Issue 1 https://doi.org/10.1186/1756-0500-5-286	journal	January 2012
GUNC: detection of chimerism and contamination in prokaryotic genomes Orakov, Askarbek; Fullam, Anthony; Coelho, Luis Pedro Genome Biology, Vol. 22, Issue 1 https://doi.org/10.1186/s13059-021-02393-0	journal	June 2021
From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria Lerat, Emmanuelle; Daubin, Vincent; Moran, Nancy A. PLoS Biology, Vol. 1, Issue 1 https://doi.org/10.1371/journal.pbio.0000019	journal	September 2003
Four families of folate-independent methionine synthases Price, Morgan N.; Deutschbauer, Adam M.; Arkin, Adam P. PLOS Genetics, Vol. 17, Issue 2 https://doi.org/10.1371/journal.pgen.1009342	journal	February 2021
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010

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59 BASIC BIOLOGICAL SCIENCES
BLAST algorithm
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database searching
genomic databases
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A fast comparative genome browser for diverse bacteria and archaea

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References (45)

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