Literature DB >> 33119741

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities.

I-Min A Chen1, Ken Chu1, Krishnaveni Palaniappan1, Anna Ratner1, Jinghua Huang1, Marcel Huntemann1, Patrick Hajek1, Stephan Ritter1, Neha Varghese1, Rekha Seshadri1, Simon Roux1, Tanja Woyke1, Emiley A Eloe-Fadrosh1, Natalia N Ivanova1, Nikos C Kyrpides1.   

Abstract

The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) contains annotated isolate genome and metagenome datasets sequenced at the DOE's Joint Genome Institute (JGI), submitted by external users, or imported from public sources such as NCBI. IMG v 6.0 includes advanced search functions and a new tool for statistical analysis of mixed sets of genomes and metagenome bins. The new IMG web user interface also has a new Help page with additional documentation and webinar tutorials to help users better understand how to use various IMG functions and tools for their research. New datasets have been processed with the prokaryotic annotation pipeline v.5, which includes extended protein family assignments. Published by Oxford University Press on behalf of Nucleic Acids Research 2020.

Entities:  

Year:  2021        PMID: 33119741      PMCID: PMC7778900          DOI: 10.1093/nar/gkaa939

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  40 in total

1.  Adaptive seeds tame genomic sequence comparison.

Authors:  Szymon M Kiełbasa; Raymond Wan; Kengo Sato; Paul Horton; Martin C Frith
Journal:  Genome Res       Date:  2011-01-05       Impact factor: 9.043

2.  The National Microbiome Data Collaborative: enabling microbiome science.

Authors:  Elisha M Wood-Charlson; Deanna Auberry; Hannah Blanco; Mark I Borkum; Yuri E Corilo; Karen W Davenport; Shweta Deshpande; Ranjeet Devarakonda; Meghan Drake; William D Duncan; Mark C Flynn; David Hays; Bin Hu; Marcel Huntemann; Po-E Li; Mary Lipton; Chien-Chi Lo; David Millard; Kayd Miller; Paul D Piehowski; Samuel Purvine; T B K Reddy; Migun Shakya; Jagadish Chandrabose Sundaramurthi; Pajau Vangay; Yaxing Wei; Bruce E Wilson; Shane Canon; Patrick S G Chain; Kjiersten Fagnan; Stanton Martin; Lee Ann McCue; Christopher J Mungall; Nigel J Mouncey; Mary E Maxon; Emiley A Eloe-Fadrosh
Journal:  Nat Rev Microbiol       Date:  2020-06       Impact factor: 60.633

3.  IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes.

Authors:  Michalis Hadjithomas; I-Min A Chen; Ken Chu; Jinghua Huang; Anna Ratner; Krishna Palaniappan; Evan Andersen; Victor Markowitz; Nikos C Kyrpides; Natalia N Ivanova
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

4.  20 years of the SMART protein domain annotation resource.

Authors:  Ivica Letunic; Peer Bork
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

5.  Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.

Authors:  Alexandre Lomsadze; Karl Gemayel; Shiyuyun Tang; Mark Borodovsky
Journal:  Genome Res       Date:  2018-05-17       Impact factor: 9.438

6.  HMMER web server: 2018 update.

Authors:  Simon C Potter; Aurélien Luciani; Sean R Eddy; Youngmi Park; Rodrigo Lopez; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

7.  The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.

Authors:  Arun Prasad Pandurangan; Jonathan Stahlhacke; Matt E Oates; Ben Smithers; Julian Gough
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

8.  The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

Authors:  Ron Caspi; Richard Billington; Luciana Ferrer; Hartmut Foerster; Carol A Fulcher; Ingrid M Keseler; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Lukas A Mueller; Quang Ong; Suzanne Paley; Pallavi Subhraveti; Daniel S Weaver; Peter D Karp
Journal:  Nucleic Acids Res       Date:  2015-11-02       Impact factor: 16.971

9.  Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.

Authors:  Rekha Seshadri; Sinead C Leahy; Graeme T Attwood; Koon Hoong Teh; Suzanne C Lambie; Adrian L Cookson; Emiley A Eloe-Fadrosh; Georgios A Pavlopoulos; Michalis Hadjithomas; Neha J Varghese; David Paez-Espino; Rechelle Perry; Gemma Henderson; Christopher J Creevey; Nicolas Terrapon; Pascal Lapebie; Elodie Drula; Vincent Lombard; Edward Rubin; Nikos C Kyrpides; Bernard Henrissat; Tanja Woyke; Natalia N Ivanova; William J Kelly
Journal:  Nat Biotechnol       Date:  2018-03-19       Impact factor: 54.908

10.  The Pfam protein families database in 2019.

Authors:  Sara El-Gebali; Jaina Mistry; Alex Bateman; Sean R Eddy; Aurélien Luciani; Simon C Potter; Matloob Qureshi; Lorna J Richardson; Gustavo A Salazar; Alfredo Smart; Erik L L Sonnhammer; Layla Hirsh; Lisanna Paladin; Damiano Piovesan; Silvio C E Tosatto; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

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  94 in total

Review 1.  The human symbiont Mucispirillum schaedleri: causality in health and disease.

Authors:  Simone Herp; Abilash Chakravarthy Durai Raj; Marta Salvado Silva; Simon Woelfel; Bärbel Stecher
Journal:  Med Microbiol Immunol       Date:  2021-05-22       Impact factor: 3.402

2.  Novel thermophilic polyhydroxyalkanoates producing strain Aneurinibacillus thermoaerophilus CCM 8960.

Authors:  Jana Musilova; Xenie Kourilova; Iva Pernicova; Matej Bezdicek; Martina Lengerova; Stanislav Obruca; Karel Sedlar
Journal:  Appl Microbiol Biotechnol       Date:  2022-06-27       Impact factor: 4.813

3.  Removal of antibiotic thiamphenicol by bacterium Aeromonas hydrophila HS01.

Authors:  Kai Yang; Sanguo Ren; Meng Mei; Yuanpei Jin; Wei Xiang; Zunji Shi; Zhihui Ai; Li Yi; Bo Xie
Journal:  World J Microbiol Biotechnol       Date:  2022-01-12       Impact factor: 3.312

4.  Petabase-scale sequence alignment catalyses viral discovery.

Authors:  Robert C Edgar; Jeff Taylor; Victor Lin; Tomer Altman; Pierre Barbera; Dmitry Meleshko; Dan Lohr; Gherman Novakovsky; Benjamin Buchfink; Basem Al-Shayeb; Jillian F Banfield; Marcos de la Peña; Anton Korobeynikov; Rayan Chikhi; Artem Babaian
Journal:  Nature       Date:  2022-01-26       Impact factor: 49.962

5.  Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14.

Authors:  Yang Li; Chengxin Zhang; Wei Zheng; Xiaogen Zhou; Eric W Bell; Dong-Jun Yu; Yang Zhang
Journal:  Proteins       Date:  2021-08-19

6.  Sinorhizobium medicae WSM419 Genes That Improve Symbiosis between Sinorhizobium meliloti Rm1021 and Medicago truncatula Jemalong A17 and in Other Symbiosis Systems.

Authors:  Prithwi Ghosh; Katie N Adolphsen; Svetlana N Yurgel; Michael L Kahn
Journal:  Appl Environ Microbiol       Date:  2021-07-13       Impact factor: 4.792

7.  Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan.

Authors:  Kazutoshi Yoshitake; Gaku Kimura; Tomoko Sakami; Tsuyoshi Watanabe; Yukiko Taniuchi; Shigeho Kakehi; Akira Kuwata; Haruyo Yamaguchi; Takafumi Kataoka; Masanobu Kawachi; Kazuho Ikeo; Engkong Tan; Yoji Igarashi; Masafumi Ohtsubo; Shugo Watabe; Yutaka Suzuki; Shuichi Asakawa; Sonoko Ishino; Kosuke Tashiro; Yoshizumi Ishino; Takanori Kobayashi; Katsuhiko Mineta; Takashi Gojobori
Journal:  Sci Rep       Date:  2021-06-09       Impact factor: 4.379

8.  Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics.

Authors:  Linta Reji; Emily L Cardarelli; Kristin Boye; John R Bargar; Christopher A Francis
Journal:  ISME J       Date:  2021-12-06       Impact factor: 10.302

Review 9.  Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution.

Authors:  Cydney N Johnson; Emma K Sheriff; Breck A Duerkop; Anushila Chatterjee
Journal:  J Bacteriol       Date:  2021-08-09       Impact factor: 3.490

10.  The Zinc Transporter ZnuABC Is Critical for the Virulence of Chromobacterium violaceum and Contributes to Diverse Zinc-Dependent Physiological Processes.

Authors:  Renato E R S Santos; Waldir P da Silva Júnior; Simone Harrison; Eric P Skaar; Walter J Chazin; José F da Silva Neto
Journal:  Infect Immun       Date:  2021-08-02       Impact factor: 3.441

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