The metagenomic telescope.

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 perfor...

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Autores principales:	Balázs Szalkai, Ildikó Scheer, Kinga Nagy, Beáta G Vértessy, Vince Grolmusz
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b08426148b304fcbbd705905954bfa94
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spelling	oai:doaj.org-article:b08426148b304fcbbd705905954bfa942021-11-25T06:07:25ZThe metagenomic telescope.1932-620310.1371/journal.pone.0101605https://doaj.org/article/b08426148b304fcbbd705905954bfa942014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25054802/?tool=EBIhttps://doaj.org/toc/1932-6203Next 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.Balázs SzalkaiIldikó ScheerKinga NagyBeáta G VértessyVince GrolmuszPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 7, p e101605 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Balázs Szalkai Ildikó Scheer Kinga Nagy Beáta G Vértessy Vince Grolmusz The metagenomic telescope.
description	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.
format	article
author	Balázs Szalkai Ildikó Scheer Kinga Nagy Beáta G Vértessy Vince Grolmusz
author_facet	Balázs Szalkai Ildikó Scheer Kinga Nagy Beáta G Vértessy Vince Grolmusz
author_sort	Balázs Szalkai
title	The metagenomic telescope.
title_short	The metagenomic telescope.
title_full	The metagenomic telescope.
title_fullStr	The metagenomic telescope.
title_full_unstemmed	The metagenomic telescope.
title_sort	metagenomic telescope.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/b08426148b304fcbbd705905954bfa94
work_keys_str_mv	AT balazsszalkai themetagenomictelescope AT ildikoscheer themetagenomictelescope AT kinganagy themetagenomictelescope AT beatagvertessy themetagenomictelescope AT vincegrolmusz themetagenomictelescope AT balazsszalkai metagenomictelescope AT ildikoscheer metagenomictelescope AT kinganagy metagenomictelescope AT beatagvertessy metagenomictelescope AT vincegrolmusz metagenomictelescope
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The metagenomic telescope.

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