MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues
[Display omitted] •MGnify Genomes is a free-to-use resource for biome-specific microbial genomes.•Each genome catalogue is non-redundant and includes extensive functional annotations.•Users can search their own sequences against the resource to assess their novelty.•MGnify Genomes can be accessed vi...
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Veröffentlicht in: | Journal of molecular biology 2023-07, Vol.435 (14), p.168016-168016, Article 168016 |
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container_title | Journal of molecular biology |
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creator | Gurbich, Tatiana A. Almeida, Alexandre Beracochea, Martin Burdett, Tony Burgin, Josephine Cochrane, Guy Raj, Shriya Richardson, Lorna Rogers, Alexander B. Sakharova, Ekaterina Salazar, Gustavo A. Finn, Robert D. |
description | [Display omitted]
•MGnify Genomes is a free-to-use resource for biome-specific microbial genomes.•Each genome catalogue is non-redundant and includes extensive functional annotations.•Users can search their own sequences against the resource to assess their novelty.•MGnify Genomes can be accessed via the website, the FTP server and the API.•The resource provides insight into previously uncultured species and novel proteins.
An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes.
Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues.
Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/. |
doi_str_mv | 10.1016/j.jmb.2023.168016 |
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•MGnify Genomes is a free-to-use resource for biome-specific microbial genomes.•Each genome catalogue is non-redundant and includes extensive functional annotations.•Users can search their own sequences against the resource to assess their novelty.•MGnify Genomes can be accessed via the website, the FTP server and the API.•The resource provides insight into previously uncultured species and novel proteins.
An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes.
Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues.
Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1016/j.jmb.2023.168016</identifier><identifier>PMID: 36806692</identifier><language>eng</language><publisher>Netherlands: Elsevier Ltd</publisher><subject>Biodiversity ; Functional annotation ; Genome, Microbial ; Metagenome - genetics ; Metagenome-assembled genome ; Metagenomics ; Microbiome ; Uncultured microorganisms</subject><ispartof>Journal of molecular biology, 2023-07, Vol.435 (14), p.168016-168016, Article 168016</ispartof><rights>2023 The Authors</rights><rights>Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.</rights><rights>2023 The Authors 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c382t-ee94999f8d1d9ece3b5b72782a4c1a8b2d03fb48182c6b075a81790cf9574e913</citedby><cites>FETCH-LOGICAL-c382t-ee94999f8d1d9ece3b5b72782a4c1a8b2d03fb48182c6b075a81790cf9574e913</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jmb.2023.168016$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,780,784,885,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36806692$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gurbich, Tatiana A.</creatorcontrib><creatorcontrib>Almeida, Alexandre</creatorcontrib><creatorcontrib>Beracochea, Martin</creatorcontrib><creatorcontrib>Burdett, Tony</creatorcontrib><creatorcontrib>Burgin, Josephine</creatorcontrib><creatorcontrib>Cochrane, Guy</creatorcontrib><creatorcontrib>Raj, Shriya</creatorcontrib><creatorcontrib>Richardson, Lorna</creatorcontrib><creatorcontrib>Rogers, Alexander B.</creatorcontrib><creatorcontrib>Sakharova, Ekaterina</creatorcontrib><creatorcontrib>Salazar, Gustavo A.</creatorcontrib><creatorcontrib>Finn, Robert D.</creatorcontrib><title>MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>[Display omitted]
•MGnify Genomes is a free-to-use resource for biome-specific microbial genomes.•Each genome catalogue is non-redundant and includes extensive functional annotations.•Users can search their own sequences against the resource to assess their novelty.•MGnify Genomes can be accessed via the website, the FTP server and the API.•The resource provides insight into previously uncultured species and novel proteins.
An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes.
Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues.
Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/.</description><subject>Biodiversity</subject><subject>Functional annotation</subject><subject>Genome, Microbial</subject><subject>Metagenome - genetics</subject><subject>Metagenome-assembled genome</subject><subject>Metagenomics</subject><subject>Microbiome</subject><subject>Uncultured microorganisms</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kUtLAzEUhYMotj5-gBuZpZupeUwniS5Ei9ZCiyC6DpnMnZoyM6nJVOi_N6W16MZV4OY75z4OQhcEDwgm-fVisGiKAcWUDUguYuUA9QkWMhU5E4eojzGlKRUs76GTEBYY4yHLxDHqsUjnuaR9NJmNW1utkzG0roFwk9wnrxDcyhtIKueTBxvLaViCsZU1ycwa7wqr650gGelO126-gnCGjipdBzjfvafo_enxbfScTl_Gk9H9NDVM0C4FkJmUshIlKSUYYMWw4JQLqjNDtChoiVlVZIIIavIC86EWhEtsKjnkGUjCTtHd1ne5KhooDbSd17Vaettov1ZOW_X3p7Ufau6-FMGMCCx5dLjaOXj3GSfvVGODgbrWLbhVUJRzIXkEs4iSLRrXDsFDte9DsNpkoBYqZqA2GahtBlFz-XvAveLn6BG43QIQz_RlwatgLLQGSuvBdKp09h_7b30AlyA</recordid><startdate>20230715</startdate><enddate>20230715</enddate><creator>Gurbich, Tatiana A.</creator><creator>Almeida, Alexandre</creator><creator>Beracochea, Martin</creator><creator>Burdett, Tony</creator><creator>Burgin, Josephine</creator><creator>Cochrane, Guy</creator><creator>Raj, Shriya</creator><creator>Richardson, Lorna</creator><creator>Rogers, Alexander B.</creator><creator>Sakharova, Ekaterina</creator><creator>Salazar, Gustavo A.</creator><creator>Finn, Robert D.</creator><general>Elsevier Ltd</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20230715</creationdate><title>MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues</title><author>Gurbich, Tatiana A. ; Almeida, Alexandre ; Beracochea, Martin ; Burdett, Tony ; Burgin, Josephine ; Cochrane, Guy ; Raj, Shriya ; Richardson, Lorna ; Rogers, Alexander B. ; Sakharova, Ekaterina ; Salazar, Gustavo A. ; Finn, Robert D.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c382t-ee94999f8d1d9ece3b5b72782a4c1a8b2d03fb48182c6b075a81790cf9574e913</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Biodiversity</topic><topic>Functional annotation</topic><topic>Genome, Microbial</topic><topic>Metagenome - genetics</topic><topic>Metagenome-assembled genome</topic><topic>Metagenomics</topic><topic>Microbiome</topic><topic>Uncultured microorganisms</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gurbich, Tatiana A.</creatorcontrib><creatorcontrib>Almeida, Alexandre</creatorcontrib><creatorcontrib>Beracochea, Martin</creatorcontrib><creatorcontrib>Burdett, Tony</creatorcontrib><creatorcontrib>Burgin, Josephine</creatorcontrib><creatorcontrib>Cochrane, Guy</creatorcontrib><creatorcontrib>Raj, Shriya</creatorcontrib><creatorcontrib>Richardson, Lorna</creatorcontrib><creatorcontrib>Rogers, Alexander B.</creatorcontrib><creatorcontrib>Sakharova, Ekaterina</creatorcontrib><creatorcontrib>Salazar, Gustavo A.</creatorcontrib><creatorcontrib>Finn, Robert D.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gurbich, Tatiana A.</au><au>Almeida, Alexandre</au><au>Beracochea, Martin</au><au>Burdett, Tony</au><au>Burgin, Josephine</au><au>Cochrane, Guy</au><au>Raj, Shriya</au><au>Richardson, Lorna</au><au>Rogers, Alexander B.</au><au>Sakharova, Ekaterina</au><au>Salazar, Gustavo A.</au><au>Finn, Robert D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>2023-07-15</date><risdate>2023</risdate><volume>435</volume><issue>14</issue><spage>168016</spage><epage>168016</epage><pages>168016-168016</pages><artnum>168016</artnum><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>[Display omitted]
•MGnify Genomes is a free-to-use resource for biome-specific microbial genomes.•Each genome catalogue is non-redundant and includes extensive functional annotations.•Users can search their own sequences against the resource to assess their novelty.•MGnify Genomes can be accessed via the website, the FTP server and the API.•The resource provides insight into previously uncultured species and novel proteins.
An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes.
Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues.
Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/.</abstract><cop>Netherlands</cop><pub>Elsevier Ltd</pub><pmid>36806692</pmid><doi>10.1016/j.jmb.2023.168016</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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source | MEDLINE; Elsevier ScienceDirect Journals Complete |
subjects | Biodiversity Functional annotation Genome, Microbial Metagenome - genetics Metagenome-assembled genome Metagenomics Microbiome Uncultured microorganisms |
title | MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues |
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