Literature DB >> 23084289

Microbial virus genome annotation-mustering the troops to fight the sequence onslaught.

J Rodney Brister1, Phillippe Le Mercier, James C Hu.   

Abstract

The revolution in virus genome sequencing promises to effectively map the extant biological universe and reveal fundamental relationships between viral biology, genome structure, and evolution. Indeed, microbial virus genomes include large numbers of conserved coding sequences of unknown function as well as unique gene combinations, implying that that these viruses will be a significant source of novel protein biochemistry and genome architecture. Yet, making sense of the approaching phalanx of A's, G's, T's, and C's stretching across the genome sequencing horizon will require innovation and an unprecedented coordination of annotation efforts among stakeholders. Published by Elsevier Inc.

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Year:  2012        PMID: 23084289      PMCID: PMC3518702          DOI: 10.1016/j.virol.2012.09.027

Source DB:  PubMed          Journal:  Virology        ISSN: 0042-6822            Impact factor:   3.616


  19 in total

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2.  Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.

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3.  The International Nucleotide Sequence Database Collaboration.

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Journal:  Nucleic Acids Res       Date:  2011-11-12       Impact factor: 16.971

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Authors:  Stephanie M Bunt; Gary B Grumbling; Helen I Field; Steven J Marygold; Nicholas H Brown; Gillian H Millburn
Journal:  Database (Oxford)       Date:  2012-05-02       Impact factor: 3.451

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Authors:  Ross Overbeek; Tadhg Begley; Ralph M Butler; Jomuna V Choudhuri; Han-Yu Chuang; Matthew Cohoon; Valérie de Crécy-Lagard; Naryttza Diaz; Terry Disz; Robert Edwards; Michael Fonstein; Ed D Frank; Svetlana Gerdes; Elizabeth M Glass; Alexander Goesmann; Andrew Hanson; Dirk Iwata-Reuyl; Roy Jensen; Neema Jamshidi; Lutz Krause; Michael Kubal; Niels Larsen; Burkhard Linke; Alice C McHardy; Folker Meyer; Heiko Neuweger; Gary Olsen; Robert Olson; Andrei Osterman; Vasiliy Portnoy; Gordon D Pusch; Dmitry A Rodionov; Christian Rückert; Jason Steiner; Rick Stevens; Ines Thiele; Olga Vassieva; Yuzhen Ye; Olga Zagnitko; Veronika Vonstein
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Authors:  Raphaël Leplae; Gipsi Lima-Mendez; Ariane Toussaint
Journal:  Nucleic Acids Res       Date:  2009-11-23       Impact factor: 16.971

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Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971

10.  The RAST Server: rapid annotations using subsystems technology.

Authors:  Ramy K Aziz; Daniela Bartels; Aaron A Best; Matthew DeJongh; Terrence Disz; Robert A Edwards; Kevin Formsma; Svetlana Gerdes; Elizabeth M Glass; Michael Kubal; Folker Meyer; Gary J Olsen; Robert Olson; Andrei L Osterman; Ross A Overbeek; Leslie K McNeil; Daniel Paarmann; Tobias Paczian; Bruce Parrello; Gordon D Pusch; Claudia Reich; Rick Stevens; Olga Vassieva; Veronika Vonstein; Andreas Wilke; Olga Zagnitko
Journal:  BMC Genomics       Date:  2008-02-08       Impact factor: 3.969

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  9 in total

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Journal:  J Biomed Inform       Date:  2017-05-10       Impact factor: 6.317

Review 2.  Crowdsourcing for bioinformatics.

Authors:  Benjamin M Good; Andrew I Su
Journal:  Bioinformatics       Date:  2013-06-19       Impact factor: 6.937

3.  NCBI viral genomes resource.

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4.  Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names.

Authors:  Jens H Kuhn; Kristian G Andersen; Yīmíng Bào; Sina Bavari; Stephan Becker; Richard S Bennett; Nicholas H Bergman; Olga Blinkova; Steven Bradfute; J Rodney Brister; Alexander Bukreyev; Kartik Chandran; Alexander A Chepurnov; Robert A Davey; Ralf G Dietzgen; Norman A Doggett; Olga Dolnik; John M Dye; Sven Enterlein; Paul W Fenimore; Pierre Formenty; Alexander N Freiberg; Robert F Garry; Nicole L Garza; Stephen K Gire; Jean-Paul Gonzalez; Anthony Griffiths; Christian T Happi; Lisa E Hensley; Andrew S Herbert; Michael C Hevey; Thomas Hoenen; Anna N Honko; Georgy M Ignatyev; Peter B Jahrling; Joshua C Johnson; Karl M Johnson; Jason Kindrachuk; Hans-Dieter Klenk; Gary Kobinger; Tadeusz J Kochel; Matthew G Lackemeyer; Daniel F Lackner; Eric M Leroy; Mark S Lever; Elke Mühlberger; Sergey V Netesov; Gene G Olinger; Sunday A Omilabu; Gustavo Palacios; Rekha G Panchal; Daniel J Park; Jean L Patterson; Janusz T Paweska; Clarence J Peters; James Pettitt; Louise Pitt; Sheli R Radoshitzky; Elena I Ryabchikova; Erica Ollmann Saphire; Pardis C Sabeti; Rachel Sealfon; Aleksandr M Shestopalov; Sophie J Smither; Nancy J Sullivan; Robert Swanepoel; Ayato Takada; Jonathan S Towner; Guido van der Groen; Viktor E Volchkov; Valentina A Volchkova; Victoria Wahl-Jensen; Travis K Warren; Kelly L Warfield; Manfred Weidmann; Stuart T Nichol
Journal:  Viruses       Date:  2014-09-26       Impact factor: 5.048

5.  An integrated ontology resource to explore and study host-virus relationships.

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6.  Virus Variation Resource - improved response to emergent viral outbreaks.

Authors:  Eneida L Hatcher; Sergey A Zhdanov; Yiming Bao; Olga Blinkova; Eric P Nawrocki; Yuri Ostapchuck; Alejandro A Schäffer; J Rodney Brister
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

7.  Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation.

Authors:  Ana Laura Grazziotin; Eugene V Koonin; David M Kristensen
Journal:  Nucleic Acids Res       Date:  2016-10-26       Impact factor: 16.971

8.  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

Authors:  Nuala A O'Leary; Mathew W Wright; J Rodney Brister; Stacy Ciufo; Diana Haddad; Rich McVeigh; Bhanu Rajput; Barbara Robbertse; Brian Smith-White; Danso Ako-Adjei; Alexander Astashyn; Azat Badretdin; Yiming Bao; Olga Blinkova; Vyacheslav Brover; Vyacheslav Chetvernin; Jinna Choi; Eric Cox; Olga Ermolaeva; Catherine M Farrell; Tamara Goldfarb; Tripti Gupta; Daniel Haft; Eneida Hatcher; Wratko Hlavina; Vinita S Joardar; Vamsi K Kodali; Wenjun Li; Donna Maglott; Patrick Masterson; Kelly M McGarvey; Michael R Murphy; Kathleen O'Neill; Shashikant Pujar; Sanjida H Rangwala; Daniel Rausch; Lillian D Riddick; Conrad Schoch; Andrei Shkeda; Susan S Storz; Hanzhen Sun; Francoise Thibaud-Nissen; Igor Tolstoy; Raymond E Tully; Anjana R Vatsan; Craig Wallin; David Webb; Wendy Wu; Melissa J Landrum; Avi Kimchi; Tatiana Tatusova; Michael DiCuccio; Paul Kitts; Terence D Murphy; Kim D Pruitt
Journal:  Nucleic Acids Res       Date:  2015-11-08       Impact factor: 16.971

9.  Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae.

Authors:  Ines Bleriot; Rocío Trastoy; Lucia Blasco; Felipe Fernández-Cuenca; Antón Ambroa; Laura Fernández-García; Olga Pacios; Elena Perez-Nadales; Julian Torre-Cisneros; Jesús Oteo-Iglesias; Ferran Navarro; Elisenda Miró; Alvaro Pascual; German Bou; Luis Martínez-Martínez; Maria Tomas
Journal:  Microb Genom       Date:  2020-04-29
  9 in total

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