MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues.
MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues.
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DOI：
10.1016/j.jmb.2023.168016
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发表时间：
2023-07-15
影响因子：
5.6
通讯作者：
Finn, Robert D.
中科院分区：
文献类型：
--
作者：
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.
关键词：
MGnify基因组是一种免费使用的生物组特定微生物基因组资源。每个基因组目录都是非冗余的，并包括广泛的功能注释。用户可以根据资源搜索他们自己的序列，以评估他们的新颖性。MGnify基因组可以通过网站、FTP服务器和API访问。该资源提供了对以前未培养的物种和新蛋白质的洞察。从散弹枪元基因组数据集的分析中产生的一个日益常见的输出是产生了元基因组组装基因组(MAG)，现在文献中描述了数万个MAG。然而，这些MAG收藏品的发现和比较因其生成、注释和存储缺乏统一性而受到阻碍。为了解决这个问题，我们开发了MGnify基因组，这是一个不断增长的生物组特定的非冗余微生物基因组目录的集合，使用MAGS和公开可用的分离基因组生成。生物组特定目录中的基因组被组织成物种簇。对于包含多个同种基因组的物种，最高质量的基因组被选为代表，总是优先考虑分离的基因组而不是MAG。物种代表性序列和注释可以在MGnify网站上可视化，完整的目录和相关的分析输出可以从MGnify服务器下载。提供了一套在线搜索工具，允许用户将自己的序列(从一个基因到几组基因组)与目录进行比较。目前有7个生物群可用，包括30,000多个基因组，代表11,048个非冗余物种，包括36个分类纲，目前没有被培养的基因组代表。MGnify基因组公司可在https://www.ebi.ac.uk/metagenomics/browse/genomes/.上获得
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/.
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影响因子：
14.9
作者：
Blum M;Chang HY;Chuguransky S;Grego T;Kandasaamy S;Mitchell A;Nuka G;Paysan-Lafosse T;Qureshi M;Raj S;Richardson L;Salazar GA;Williams L;Bork P;Bridge A;Gough J;Haft DH;Letunic I;Marchler-Bauer A;Mi H;Natale DA;Necci M;Orengo CA;Pandurangan AP;Rivoire C;Sigrist CJA;Sillitoe I;Thanki N;Thomas PD;Tosatto SCE;Wu CH;Bateman A;Finn RD
通讯作者：
Finn RD
影响因子：
14.9
作者：
Mistry J;Chuguransky S;Williams L;Qureshi M;Salazar GA;Sonnhammer ELL;Tosatto SCE;Paladin L;Raj S;Richardson LJ;Finn RD;Bateman A
通讯作者：
Bateman A
DOI：
10.1016/j.xgen.2022.100123
发表时间：
2022-05-11
期刊：
CELL GENOMICS
影响因子：
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作者：
Delmont, Tom O.;Gaia, Morgan;Hinsinger, Damien D.;Fremont, Paul;Vanni, Chiara;Fernandez-Guerra, Antonio;Eren, A. Murat;Kourlaiev, Artem;d'Agata, Leo;Clayssen, Quentin;Villar, Emilie;Labadie, Karine;Cruaud, Corinne;Poulain, Julie;Da Silva, Corinne;Wessner, Marc;Noel, Benjamin;Aury, Jean-Marc;de Vargas, Colomban;Bowler, Chris;Karsenti, Eric;Pelletier, Eric;Wincker, Patrick;Jaillon, Olivier
通讯作者：
Jaillon, Olivier
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DOI：
10.1093/bioinformatics/btt509
发表时间：
2013-11-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
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作者：
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通讯作者：
Eddy SR
影响因子：
14.9
作者：
Chen IA;Chu K;Palaniappan K;Pillay M;Ratner A;Huang J;Huntemann M;Varghese N;White JR;Seshadri R;Smirnova T;Kirton E;Jungbluth SP;Woyke T;Eloe-Fadrosh EA;Ivanova NN;Kyrpides NC
通讯作者：
Kyrpides NC