Literature DB >> 25414350

GenBank.

Dennis A Benson1, Karen Clark1, Ilene Karsch-Mizrachi1, David J Lipman1, James Ostell1, Eric W Sayers2.   

Abstract

GenBank(®) (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by US Government employees and is in the public domain in the US.

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Mesh:

Year:  2014        PMID: 25414350      PMCID: PMC4383990          DOI: 10.1093/nar/gku1216

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   19.160


  16 in total

1.  Protein sequence similarity searches using patterns as seeds.

Authors:  Z Zhang; A A Schäffer; W Miller; T L Madden; D J Lipman; E V Koonin; S F Altschul
Journal:  Nucleic Acids Res       Date:  1998-09-01       Impact factor: 16.971

Review 2.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

3.  Functional annotation of a full-length mouse cDNA collection.

Authors:  J Kawai; A Shinagawa; K Shibata; M Yoshino; M Itoh; Y Ishii; T Arakawa; A Hara; Y Fukunishi; H Konno; J Adachi; S Fukuda; K Aizawa; M Izawa; K Nishi; H Kiyosawa; S Kondo; I Yamanaka; T Saito; Y Okazaki; T Gojobori; H Bono; T Kasukawa; R Saito; K Kadota; H Matsuda; M Ashburner; S Batalov; T Casavant; W Fleischmann; T Gaasterland; C Gissi; B King; H Kochiwa; P Kuehl; S Lewis; Y Matsuo; I Nikaido; G Pesole; J Quackenbush; L M Schriml; F Staubli; R Suzuki; M Tomita; L Wagner; T Washio; K Sakai; T Okido; M Furuno; H Aono; R Baldarelli; G Barsh; J Blake; D Boffelli; N Bojunga; P Carninci; M F de Bonaldo; M J Brownstein; C Bult; C Fletcher; M Fujita; M Gariboldi; S Gustincich; D Hill; M Hofmann; D A Hume; M Kamiya; N H Lee; P Lyons; L Marchionni; J Mashima; J Mazzarelli; P Mombaerts; P Nordone; B Ring; M Ringwald; I Rodriguez; N Sakamoto; H Sasaki; K Sato; C Schönbach; T Seya; Y Shibata; K F Storch; H Suzuki; K Toyo-oka; K H Wang; C Weitz; C Whittaker; L Wilming; A Wynshaw-Boris; K Yoshida; Y Hasegawa; H Kawaji; S Kohtsuki; Y Hayashizaki
Journal:  Nature       Date:  2001-02-08       Impact factor: 49.962

4.  The NCBI Taxonomy database.

Authors:  Scott Federhen
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

5.  The Sequence Read Archive: explosive growth of sequencing data.

Authors:  Yuichi Kodama; Martin Shumway; Rasko Leinonen
Journal:  Nucleic Acids Res       Date:  2011-10-18       Impact factor: 16.971

6.  BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.

Authors:  Tanya Barrett; Karen Clark; Robert Gevorgyan; Vyacheslav Gorelenkov; Eugene Gribov; Ilene Karsch-Mizrachi; Michael Kimelman; Kim D Pruitt; Sergei Resenchuk; Tatiana Tatusova; Eugene Yaschenko; James Ostell
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

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

Authors: 
Journal:  Nucleic Acids Res       Date:  2013-11-19       Impact factor: 16.971

8.  BLAST: a more efficient report with usability improvements.

Authors:  Grzegorz M Boratyn; Christiam Camacho; Peter S Cooper; George Coulouris; Amelia Fong; Ning Ma; Thomas L Madden; Wayne T Matten; Scott D McGinnis; Yuri Merezhuk; Yan Raytselis; Eric W Sayers; Tao Tao; Jian Ye; Irena Zaretskaya
Journal:  Nucleic Acids Res       Date:  2013-04-22       Impact factor: 16.971

9.  The International Nucleotide Sequence Database Collaboration.

Authors:  Yasukazu Nakamura; Guy Cochrane; Ilene Karsch-Mizrachi
Journal:  Nucleic Acids Res       Date:  2012-11-24       Impact factor: 16.971

10.  DDBJ progress report: a new submission system for leading to a correct annotation.

Authors:  Takehide Kosuge; Jun Mashima; Yuichi Kodama; Takatomo Fujisawa; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Toshihisa Takagi; Yasukazu Nakamura
Journal:  Nucleic Acids Res       Date:  2013-11-04       Impact factor: 16.971

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  185 in total

1.  BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.

Authors:  Michael J Meyer; Philip Geske; Haiyuan Yu
Journal:  Bioinformatics       Date:  2016-01-23       Impact factor: 6.937

2.  OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Authors:  Jasmine Y Young; John D Westbrook; Zukang Feng; Raul Sala; Ezra Peisach; Thomas J Oldfield; Sanchayita Sen; Aleksandras Gutmanas; David R Armstrong; John M Berrisford; Li Chen; Minyu Chen; Luigi Di Costanzo; Dimitris Dimitropoulos; Guanghua Gao; Sutapa Ghosh; Swanand Gore; Vladimir Guranovic; Pieter M S Hendrickx; Brian P Hudson; Reiko Igarashi; Yasuyo Ikegawa; Naohiro Kobayashi; Catherine L Lawson; Yuhe Liang; Steve Mading; Lora Mak; M Saqib Mir; Abhik Mukhopadhyay; Ardan Patwardhan; Irina Persikova; Luana Rinaldi; Eduardo Sanz-Garcia; Monica R Sekharan; Chenghua Shao; G Jawahar Swaminathan; Lihua Tan; Eldon L Ulrich; Glen van Ginkel; Reiko Yamashita; Huanwang Yang; Marina A Zhuravleva; Martha Quesada; Gerard J Kleywegt; Helen M Berman; John L Markley; Haruki Nakamura; Sameer Velankar; Stephen K Burley
Journal:  Structure       Date:  2017-02-09       Impact factor: 5.006

3.  Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

Authors:  Brinda Vallat; Benjamin Webb; John D Westbrook; Andrej Sali; Helen M Berman
Journal:  Structure       Date:  2018-04-12       Impact factor: 5.006

4.  Molecular and morphological description of Haemoproteus (Parahaemoproteus) bukaka (species nova), a haemosporidian associated with the strictly Australo-Papuan host subfamily Cracticinae.

Authors:  W Goulding; R D Adlard; S M Clegg; N J Clark
Journal:  Parasitol Res       Date:  2016-05-12       Impact factor: 2.289

Review 5.  Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.

Authors:  John A Gerlt; Jason T Bouvier; Daniel B Davidson; Heidi J Imker; Boris Sadkhin; David R Slater; Katie L Whalen
Journal:  Biochim Biophys Acta       Date:  2015-04-18

6.  Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases.

Authors:  Chung F Wong
Journal:  Protein Sci       Date:  2015-06-22       Impact factor: 6.725

7.  Phylogenetic sequence analysis and functional studies reveal compensatory amino acid substitutions in loop 2 of human ribonucleotide reductase.

Authors:  Andrew J Knappenberger; Sneha Grandhi; Reena Sheth; Md Faiz Ahmad; Rajesh Viswanathan; Michael E Harris
Journal:  J Biol Chem       Date:  2017-08-14       Impact factor: 5.157

8.  MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.

Authors:  Ranko Gacesa; Jurica Zucko; Solveig K Petursdottir; Elisabet Eik Gudmundsdottir; Olafur H Fridjonsson; Janko Diminic; Paul F Long; John Cullum; Daslav Hranueli; Gudmundur O Hreggvidsson; Antonio Starcevic
Journal:  Food Technol Biotechnol       Date:  2017-06       Impact factor: 3.918

9.  Early evolutionary loss of the lipid A modifying enzyme PagP resulting in innate immune evasion in Yersinia pestis.

Authors:  Courtney E Chandler; Erin M Harberts; Mark R Pelletier; Iyarit Thaipisuttikul; Jace W Jones; Adeline M Hajjar; Jason W Sahl; David R Goodlett; Aaron C Pride; David A Rasko; M Stephen Trent; Russell E Bishop; Robert K Ernst
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-31       Impact factor: 11.205

10.  Prediction of Burkholderia pseudomallei DsbA substrates identifies potential virulence factors and vaccine targets.

Authors:  Ben Vezina; Guillaume A Petit; Jennifer L Martin; Maria A Halili
Journal:  PLoS One       Date:  2020-11-20       Impact factor: 3.240

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