Literature DB >> 31602479

Database resources of the National Center for Biotechnology Information.

Eric W Sayers1, Jeff Beck1, J Rodney Brister1, Evan E Bolton1, Kathi Canese1, Donald C Comeau1, Kathryn Funk1, Anne Ketter1, Sunghwan Kim1, Avi Kimchi1, Paul A Kitts1, Anatoliy Kuznetsov1, Stacy Lathrop1, Zhiyong Lu1, Kelly McGarvey1, Thomas L Madden1, Terence D Murphy1, Nuala O'Leary1, Lon Phan1, Valerie A Schneider1, Françoise Thibaud-Nissen1, Bart W Trawick1, Kim D Pruitt1, James Ostell1.   

Abstract

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface, a sequence database search and a gene orthologs page. Additional resources that were updated in the past year include PMC, Bookshelf, My Bibliography, Assembly, RefSeq, viral genomes, the prokaryotic genome annotation pipeline, Genome Workbench, dbSNP, BLAST, Primer-BLAST, IgBLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2019.

Entities:  

Mesh:

Year:  2020        PMID: 31602479      PMCID: PMC6943063          DOI: 10.1093/nar/gkz899

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


  25 in total

1.  dbSNP: a database of single nucleotide polymorphisms.

Authors:  E M Smigielski; K Sirotkin; M Ward; S T Sherry
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

Authors:  Kazutaka Katoh; Kazuharu Misawa; Kei-ichi Kuma; Takashi Miyata
Journal:  Nucleic Acids Res       Date:  2002-07-15       Impact factor: 16.971

3.  Entrez: molecular biology database and retrieval system.

Authors:  G D Schuler; J A Epstein; H Ohkawa; J A Kans
Journal:  Methods Enzymol       Date:  1996       Impact factor: 1.600

4.  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

5.  Best Match: New relevance search for PubMed.

Authors:  Nicolas Fiorini; Kathi Canese; Grisha Starchenko; Evgeny Kireev; Won Kim; Vadim Miller; Maxim Osipov; Michael Kholodov; Rafis Ismagilov; Sunil Mohan; James Ostell; Zhiyong Lu
Journal:  PLoS Biol       Date:  2018-08-28       Impact factor: 8.029

6.  Database resources of the National Center for Biotechnology Information.

Authors:  Eric W Sayers; Richa Agarwala; Evan E Bolton; J Rodney Brister; Kathi Canese; Karen Clark; Ryan Connor; Nicolas Fiorini; Kathryn Funk; Timothy Hefferon; J Bradley Holmes; Sunghwan Kim; Avi Kimchi; Paul A Kitts; Stacy Lathrop; Zhiyong Lu; Thomas L Madden; Aron Marchler-Bauer; Lon Phan; Valerie A Schneider; Conrad L Schoch; Kim D Pruitt; James Ostell
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

7.  The European Nucleotide Archive in 2018.

Authors:  Peter W Harrison; Blaise Alako; Clara Amid; Ana Cerdeño-Tárraga; Iain Cleland; Sam Holt; Abdulrahman Hussein; Suran Jayathilaka; Simon Kay; Thomas Keane; Rasko Leinonen; Xin Liu; Josué Martínez-Villacorta; Annalisa Milano; Nima Pakseresht; Jeena Rajan; Kethi Reddy; Edward Richards; Marc Rosello; Nicole Silvester; Dmitriy Smirnov; Ana-Luisa Toribio; Senthilnathan Vijayaraja; Guy Cochrane
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

8.  PUG-View: programmatic access to chemical annotations integrated in PubChem.

Authors:  Sunghwan Kim; Paul A Thiessen; Tiejun Cheng; Jian Zhang; Asta Gindulyte; Evan E Bolton
Journal:  J Cheminform       Date:  2019-08-09       Impact factor: 5.514

9.  IgBLAST: an immunoglobulin variable domain sequence analysis tool.

Authors:  Jian Ye; Ning Ma; Thomas L Madden; James M Ostell
Journal:  Nucleic Acids Res       Date:  2013-05-13       Impact factor: 16.971

10.  NCBI prokaryotic genome annotation pipeline.

Authors:  Tatiana Tatusova; Michael DiCuccio; Azat Badretdin; Vyacheslav Chetvernin; Eric P Nawrocki; Leonid Zaslavsky; Alexandre Lomsadze; Kim D Pruitt; Mark Borodovsky; James Ostell
Journal:  Nucleic Acids Res       Date:  2016-06-24       Impact factor: 16.971

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  113 in total

1.  High-throughput cultivation and identification of bacteria from the plant root microbiota.

Authors:  Jingying Zhang; Yong-Xin Liu; Xiaoxuan Guo; Yuan Qin; Ruben Garrido-Oter; Paul Schulze-Lefert; Yang Bai
Journal:  Nat Protoc       Date:  2021-01-13       Impact factor: 13.491

2.  The Protein Data Bank Archive.

Authors:  Sameer Velankar; Stephen K Burley; Genji Kurisu; Jeffrey C Hoch; John L Markley
Journal:  Methods Mol Biol       Date:  2021

Review 3.  Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data.

Authors:  Kihyun Lee; Dae-Wi Kim; Chang-Jun Cha
Journal:  J Microbiol       Date:  2021-02-23       Impact factor: 3.422

4.  Different Susceptibility of T and B Cells to Cladribine Depends On Their Levels of Deoxycytidine Kinase Activity Linked to Activation Status.

Authors:  Federico Carlini; Federico Ivaldi; Francesca Gualandi; Ursula Boschert; Diego Centonze; Giuseppe Matarese; Marco Salvetti; Nicole Kerlero de Rosbo; Antonio Uccelli
Journal:  J Neuroimmune Pharmacol       Date:  2021-04-14       Impact factor: 4.147

5.  Building a tRNA thermometer to estimate microbial adaptation to temperature.

Authors:  Emre Cimen; Sarah E Jensen; Edward S Buckler
Journal:  Nucleic Acids Res       Date:  2020-12-02       Impact factor: 16.971

Review 6.  NCBI Taxonomy: a comprehensive update on curation, resources and tools.

Authors:  Conrad L Schoch; Stacy Ciufo; Mikhail Domrachev; Carol L Hotton; Sivakumar Kannan; Rogneda Khovanskaya; Detlef Leipe; Richard Mcveigh; Kathleen O'Neill; Barbara Robbertse; Shobha Sharma; Vladimir Soussov; John P Sullivan; Lu Sun; Seán Turner; Ilene Karsch-Mizrachi
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

7.  Holin-Dependent Secretion of the Large Clostridial Toxin TpeL by Clostridium perfringens.

Authors:  Angela Saadat; Stephen B Melville
Journal:  J Bacteriol       Date:  2021-03-23       Impact factor: 3.490

8.  Morphological and molecular characterization of a novel Myxobolus species from the gastrointestinal tract of brown trout (Salmo trutta) in Spain.

Authors:  Seila Couso-Pérez; Luis F Rangel; Maria J Santos; Elvira Ares-Mazás; Hipólito Gómez-Couso
Journal:  Parasitol Res       Date:  2021-06-21       Impact factor: 2.289

9.  Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens.

Authors:  Alexander Kraus; Mareen Weskamp; Jennifer Zierles; Miriam Balzer; Ramona Busch; Jessica Eisfeld; Jan Lambertz; Marc M Nowaczyk; Franz Narberhaus
Journal:  J Bacteriol       Date:  2020-10-22       Impact factor: 3.490

10.  Automated generation of gene summaries at the Alliance of Genome Resources.

Authors:  Ranjana Kishore; Valerio Arnaboldi; Ceri E Van Slyke; Juancarlos Chan; Robert S Nash; Jose M Urbano; Mary E Dolan; Stacia R Engel; Mary Shimoyama; Paul W Sternberg; The Alliance Of Genome Resources
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

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