The IMG/M data management and analysis system v.7: content updates and new features

Chen, I-Min A.; Chu, Ken; Palaniappan, Krishnaveni; Ratner, Anna; Huang, Jinghua; Huntemann, Marcel; Hajek, Patrick; Ritter, Stephan J; Webb, Cody; Wu, Dongying; Varghese, Neha J; Reddy, T. K.; Mukherjee, Supratim; Ovchinnikova, Galina; Nolan, Matt; Seshadri, Rekha; Roux, Simon; Visel, Axel; Woyke, Tanja; Eloe-Fadrosh, Emiley A; Kyrpides, Nikos C; Ivanova, Natalia N

doi:10.1093/nar/gkac976

Title: The IMG/M data management and analysis system v.7: content updates and new features

Abstract

The Integrated Microbial Genomes & Microbiomes system at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. Here, we also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).

Authors:

^[1]; Chu, Ken ^[1]; Palaniappan, Krishnaveni ^[1]; Ratner, Anna ^[1]; Huang, Jinghua ^[1];

^[1]; Hajek, Patrick ^[1]; Ritter, Stephan J ^[1]; Webb, Cody ^[1]; Wu, Dongying ^[1]; Varghese, Neha J ^[1];

^[1];

^[1]; Nolan, Matt ^[1]; Seshadri, Rekha ^[1];

^[1]; Visel, Axel ^[1]; Woyke, Tanja ^[1];

^[1] more »

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint Genome Institute

Publication Date:: Wed Nov 16 00:00:00 EST 2022

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

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

OSTI Identifier:: 1907597

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Nucleic Acids Research

Additional Journal Information:: Journal Volume: 51; Journal Issue: D1; Journal ID: ISSN 0305-1048

Publisher:: Oxford University Press

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Chen, I-Min A., Chu, Ken, Palaniappan, Krishnaveni, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Hajek, Patrick, Ritter, Stephan J, Webb, Cody, Wu, Dongying, Varghese, Neha J, Reddy, T. K., Mukherjee, Supratim, Ovchinnikova, Galina, Nolan, Matt, Seshadri, Rekha, Roux, Simon, Visel, Axel, Woyke, Tanja, Eloe-Fadrosh, Emiley A, Kyrpides, Nikos C, and Ivanova, Natalia N. The IMG/M data management and analysis system v.7: content updates and new features.  United States: N. p., 2022. 
Web.  doi:10.1093/nar/gkac976.

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                    Chen, I-Min A., Chu, Ken, Palaniappan, Krishnaveni, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Hajek, Patrick, Ritter, Stephan J, Webb, Cody, Wu, Dongying, Varghese, Neha J, Reddy, T. K., Mukherjee, Supratim, Ovchinnikova, Galina, Nolan, Matt, Seshadri, Rekha, Roux, Simon, Visel, Axel, Woyke, Tanja, Eloe-Fadrosh, Emiley A, Kyrpides, Nikos C, & Ivanova, Natalia N. The IMG/M data management and analysis system v.7: content updates and new features.  United States.  https://doi.org/10.1093/nar/gkac976

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                    Chen, I-Min A., Chu, Ken, Palaniappan, Krishnaveni, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Hajek, Patrick, Ritter, Stephan J, Webb, Cody, Wu, Dongying, Varghese, Neha J, Reddy, T. K., Mukherjee, Supratim, Ovchinnikova, Galina, Nolan, Matt, Seshadri, Rekha, Roux, Simon, Visel, Axel, Woyke, Tanja, Eloe-Fadrosh, Emiley A, Kyrpides, Nikos C, and Ivanova, Natalia N. Wed .  
"The IMG/M data management and analysis system v.7: content updates and new features".  United States.  https://doi.org/10.1093/nar/gkac976.  https://www.osti.gov/servlets/purl/1907597.

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@article{osti_1907597,

  title        = {The IMG/M data management and analysis system v.7: content updates and new features},

  author       = {Chen, I-Min A. and Chu, Ken and Palaniappan, Krishnaveni and Ratner, Anna and Huang, Jinghua and Huntemann, Marcel and Hajek, Patrick and Ritter, Stephan J and Webb, Cody and Wu, Dongying and Varghese, Neha J and Reddy, T. K. and Mukherjee, Supratim and Ovchinnikova, Galina and Nolan, Matt and Seshadri, Rekha and Roux, Simon and Visel, Axel and Woyke, Tanja and Eloe-Fadrosh, Emiley A and Kyrpides, Nikos C and Ivanova, Natalia N},

  abstractNote = {The Integrated Microbial Genomes & Microbiomes system at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. Here, we also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).},

  doi          = {10.1093/nar/gkac976},

  journal      = {Nucleic Acids Research},

  number       = D1,

  volume       = 51,

  place        = {United States},

  year         = {Wed Nov 16 00:00:00 EST 2022},

  month        = {Wed Nov 16 00:00:00 EST 2022}

}

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Title: The IMG/M data management and analysis system v.7: content updates and new features

Abstract

Citation Formats

DOE JGI Metagenome Workflow journal, June 2021

Adaptive seeds tame genomic sequence comparison journal, January 2011

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures journal, March 2015

Genomes OnLine Database (GOLD) v.8: overview and updates journal, November 2020

KBase: The United States Department of Energy Systems Biology Knowledgebase journal, July 2018

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats journal, June 2007

Improved metagenomic analysis with Kraken 2 journal, November 2019

The MetaCyc database of metabolic pathways and enzymes - a 2019 update journal, October 2019

Origin and Evolution of Nitrogen Fixation in Prokaryotes journal, August 2022

20 years of the SMART protein domain annotation resource journal, October 2017

UniProt: the universal protein knowledgebase in 2021 journal, November 2020

Rfam: annotating non-coding RNAs in complete genomes journal, December 2004

GenBank journal, November 2017

TIGRFAMs and Genome Properties in 2013 journal, November 2012

SignalP 4.0: discriminating signal peptides from transmembrane regions journal, September 2011

KEGG: integrating viruses and cellular organisms journal, October 2020

The Sequence Read Archive journal, November 2010

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes journal, August 2021

Centrifuge: rapid and sensitive classification of metagenomic sequences journal, October 2016

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The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver journal, November 2018

CATH: expanding the horizons of structure-based functional annotations for genome sequences journal, November 2018

Prodigal: prokaryotic gene recognition and translation initiation site identification journal, March 2010

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HMMER web server: 2018 update journal, June 2018

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Genomes OnLine Database (GOLD) v.8: overview and updates
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KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
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Improved metagenomic analysis with Kraken 2
journal, November 2019

The MetaCyc database of metabolic pathways and enzymes - a 2019 update
journal, October 2019

Origin and Evolution of Nitrogen Fixation in Prokaryotes
journal, August 2022

20 years of the SMART protein domain annotation resource
journal, October 2017

UniProt: the universal protein knowledgebase in 2021
journal, November 2020

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journal, December 2004

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TIGRFAMs and Genome Properties in 2013
journal, November 2012

SignalP 4.0: discriminating signal peptides from transmembrane regions
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KEGG: integrating viruses and cellular organisms
journal, October 2020

The Sequence Read Archive
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tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
journal, August 2021

Centrifuge: rapid and sensitive classification of metagenomic sequences
journal, October 2016

COG database update: focus on microbial diversity, model organisms, and widespread pathogens
journal, November 2020

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver
journal, November 2018

CATH: expanding the horizons of structure-based functional annotations for genome sequences
journal, November 2018

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
journal, October 2018

HMMER web server: 2018 update
journal, June 2018

The Gene Ontology resource: enriching a GOld mine
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Microbial species delineation using whole genome sequences
journal, July 2015

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
journal, November 2014

Infernal 1.1: 100-fold faster RNA homology searches
journal, September 2013

Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes
journal, January 2005

Infernal 1.0: inference of RNA alignments
journal, March 2009

Evidence for Nitrogen Fixation by “ Dehalococcoides ethenogenes ” Strain 195
journal, December 2009

InCHlib – interactive cluster heatmap for web applications
journal, September 2014

Interactive metagenomic visualization in a Web browser
journal, September 2011

The InterPro protein families and domains database: 20 years on
journal, November 2020

Pfam: The protein families database in 2021
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IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
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journal, July 2001