The Metagenomic Telescope
Publication Date
July 23, 2014
Journal
PLOS ONE
Authors
Balázs Szalkai, Ildikó Scheer, Kinga Nagy, Beáta G. Vértessy, et al
Volume
9
Issue
7
Pages
e101605
DOI
http://doi.org/10.1371/journal.pone.0101605
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0101605
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25054802
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108317
Europe PMC
http://europepmc.org/abstract/MED/25054802
Web of Science
000339614100016
Scopus
84904639125
Mendeley
http://www.mendeley.com/research/metagenomic-telescope
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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1606340"], "description"=>"<p>Projection 1 discovers genes or proteins in the metagenome that probably have similar function as the well-known starting proteins in front of the objective lens on the right hand side. Projection 2 directly identifies these proteins within the proteomes of the model organisms (as a set of UniProt accession numbers).</p>", "links"=>[], "tags"=>["Computational biology", "genetics", "genomics", "metagenomics", "Model organisms", "compared", "metagenomic"], "article_id"=>1115490, "categories"=>["Biological Sciences"], "users"=>["Balázs Szalkai", "Ildikó Scheer", "Kinga Nagy", "Beáta G. Vértessy", "Vince Grolmusz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101605.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_original_projection_upper_panel_compared_to_the_scheme_of_the_Metagenomic_Telescope_lower_panel_/1115490", "title"=>"The original projection (upper panel) compared to the scheme of the Metagenomic Telescope (lower panel).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 03:32:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1606341"], "description"=>"<p>The flowchart of the Metagenomic Telescope applied to DNA repair enzymes.</p>", "links"=>[], "tags"=>["Computational biology", "genetics", "genomics", "metagenomics", "Model organisms", "flowchart", "metagenomic", "applied", "dna"], "article_id"=>1115491, "categories"=>["Biological Sciences"], "users"=>["Balázs Szalkai", "Ildikó Scheer", "Kinga Nagy", "Beáta G. Vértessy", "Vince Grolmusz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101605.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_flowchart_of_the_Metagenomic_Telescope_applied_to_DNA_repair_enzymes_/1115491", "title"=>"The flowchart of the Metagenomic Telescope applied to DNA repair enzymes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 03:32:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1606342"], "description"=>"<p>Panel A shows an alignment (created by ClustalW) between the mouse dUTPase sequence (cyan) and the novel hit associated with the Uniprot accession number Q3TL09 (purple color indicates the part of this latter sequence that could be modeled in 3D using SwissModel or MUSTER). The conserved dUTPase motifs are shown in yellow. Panel B illustrates the structural alignment between human dUTPase (cyan) and the Q3TL09 modeled structure (purple) (at the subunit level). Panel C shows one of the models for Q3TL09 created by MUSTER software (purple), in this case the trimeric structure characteristic of dUTPases is shown (monomers are in shades of blue: cyan, royal blue and grayish blue). Protein structural models are shown in ribbon diagrams (PyMol).</p>", "links"=>[], "tags"=>["Computational biology", "genetics", "genomics", "metagenomics", "Model organisms", "dutpase-like", "proteome", "metagenomic"], "article_id"=>1115492, "categories"=>["Biological Sciences"], "users"=>["Balázs Szalkai", "Ildikó Scheer", "Kinga Nagy", "Beáta G. Vértessy", "Vince Grolmusz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101605.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_a_novel_dUTPase_like_protein_in_the_mouse_proteome_using_the_Metagenomic_Telescope_/1115492", "title"=>"Identification of a novel dUTPase-like protein in the mouse proteome using the Metagenomic Telescope.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 03:32:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1606343"], "description"=>"<p>(A) Mre11 has five phosphodiesterase motifs (green), 6 dsDNA recognition loop (yellow) and hydrophobic surface clusters (grey) (B) Rad50 has a bipartite ATPase domain: Walker A (red), Walker B (pale red), Q-loop (light blue), ABC-Signature motif (orange), histidine switch (green H) and has a Zinc-hook (purple).</p>", "links"=>[], "tags"=>["Computational biology", "genetics", "genomics", "metagenomics", "Model organisms", "mre11", "rad50"], "article_id"=>1115493, "categories"=>["Biological Sciences"], "users"=>["Balázs Szalkai", "Ildikó Scheer", "Kinga Nagy", "Beáta G. Vértessy", "Vince Grolmusz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101605.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_Mre11_Panel_A_and_Rad50_Panel_B_domains_/1115493", "title"=>"Schematic representation of Mre11 (Panel A) and Rad50 (Panel B) domains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 03:32:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1606344"], "description"=>"<p>Panel A. Number of hits identified in the various eukaryotic model organisms after the original and the telescopic projections. Panel B. Distribution of genome ontology terms within the different hits. Note that new genome ontology classes can be observed in the telescopic hits.</p>", "links"=>[], "tags"=>["Computational biology", "genetics", "genomics", "metagenomics", "Model organisms", "telescopic", "hits", "mre11"], "article_id"=>1115494, "categories"=>["Biological Sciences"], "users"=>["Balázs Szalkai", "Ildikó Scheer", "Kinga Nagy", "Beáta G. Vértessy", "Vince Grolmusz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101605.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Original_and_telescopic_hits_for_the_Mre11_family_/1115494", "title"=>"Original and telescopic hits for the Mre11 family.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 03:32:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1606345"], "description"=>"<p>Panel A. Number of hits identified in the various eukaryotic model organisms after the original and the telescopic projections. Panel B. Distribution of genome ontology terms within the different hits. Note that new genome ontology classes can be observed in the telescopic hits.</p>", "links"=>[], "tags"=>["Computational biology", "genetics", "genomics", "metagenomics", "Model organisms", "telescopic", "hits", "rad50"], "article_id"=>1115495, "categories"=>["Biological Sciences"], "users"=>["Balázs Szalkai", "Ildikó Scheer", "Kinga Nagy", "Beáta G. Vértessy", "Vince Grolmusz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101605.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Original_and_telescopic_hits_for_the_Rad50_family_/1115495", "title"=>"Original and telescopic hits for the Rad50 family.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-23 03:32:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1606346"], "description"=>"<p>Protein families and proteomes used in the present study.</p>", "links"=>[], "tags"=>["Computational biology", "genetics", "genomics", "metagenomics", "Model organisms", "proteomes"], "article_id"=>1115496, "categories"=>["Biological Sciences"], "users"=>["Balázs Szalkai", "Ildikó Scheer", "Kinga Nagy", "Beáta G. Vértessy", "Vince Grolmusz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101605.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_families_and_proteomes_used_in_the_present_study_/1115496", "title"=>"Protein families and proteomes used in the present study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-23 03:32:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1606347"], "description"=>"<p>Using Rad50 sequences to build the starting HMM model, the Metagenomic Telescope approach identified the new telescopic hits listed in the table.</p>", "links"=>[], "tags"=>["Computational biology", "genetics", "genomics", "metagenomics", "Model organisms", "telescopic", "hits", "transcription"], "article_id"=>1115497, "categories"=>["Biological Sciences"], "users"=>["Balázs Szalkai", "Ildikó Scheer", "Kinga Nagy", "Beáta G. Vértessy", "Vince Grolmusz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101605.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_New_telescopic_hits_associated_with_a_role_in_transcription_regulation_/1115497", "title"=>"New telescopic hits associated with a role in transcription regulation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-23 03:32:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1606348"], "description"=>"<div><p>Next generation sequencing technologies led to the discovery of numerous new microbe species in diverse environmental samples. Some of the new species contain genes never encountered before. Some of these genes encode proteins with novel functions, and some of these genes encode proteins that perform some well-known function in a novel way. A tool, named the Metagenomic Telescope, is described here that applies artificial intelligence methods, and seems to be capable of identifying new protein functions even in the well-studied model organisms. As a proof-of-principle demonstration of the Metagenomic Telescope, we considered DNA repair enzymes in the present work. First we identified proteins in DNA repair in well–known organisms (i.e., proteins in base excision repair, nucleotide excision repair, mismatch repair and DNA break repair); next we applied multiple alignments and then built hidden Markov profiles for each protein separately, across well–researched organisms; next, using public depositories of metagenomes, originating from extreme environments, we identified DNA repair genes in the samples. While the phylogenetic classification of the metagenomic samples are not typically available, we hypothesized that some very special DNA repair strategies need to be applied in bacteria and Archaea living in those extreme circumstances. It is a difficult task to evaluate the results obtained from mostly unknown species; therefore we applied again the hidden Markov profiling: for the identified DNA repair genes in the extreme metagenomes, we prepared new hidden Markov profiles (for each genes separately, subsequent to a cluster analysis); and we searched for similarities to those profiles in model organisms. We have found well known DNA repair proteins, numerous proteins with unknown functions, and also proteins with known, but different functions in the model organisms.</p></div>", "links"=>[], "tags"=>["Computational biology", "genetics", "genomics", "metagenomics", "Model organisms", "metagenomic"], "article_id"=>1115498, "categories"=>["Biological Sciences"], "users"=>["Balázs Szalkai", "Ildikó Scheer", "Kinga Nagy", "Beáta G. Vértessy", "Vince Grolmusz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101605"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Metagenomic_Telescope_/1115498", "title"=>"The Metagenomic Telescope", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-23 03:32:46"}

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Relative Metric

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