Literature DB >> 14681350

GenBank: update.

Dennis A Benson1, Ilene Karsch-Mizrachi, David J Lipman, James Ostell, David L Wheeler.   

Abstract

GenBank is a comprehensive database that contains publicly available DNA sequences for more than 140 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin program and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, 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. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Mesh:

Year:  2004        PMID: 14681350      PMCID: PMC308779          DOI: 10.1093/nar/gkh045

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


  11 in total

1.  MMDB: Entrez's 3D-structure database.

Authors:  Jie Chen; John B Anderson; Carol DeWeese-Scott; Natalie D Fedorova; Lewis Y Geer; Siqian He; David I Hurwitz; John D Jackson; Aviva R Jacobs; Christopher J Lanczycki; Cynthia A Liebert; Chunlei Liu; Thomas Madej; Aron Marchler-Bauer; Gabriele H Marchler; Raja Mazumder; Anastasia N Nikolskaya; Bachoti S Rao; Anna R Panchenko; Benjamin A Shoemaker; Vahan Simonyan; James S Song; Paul A Thiessen; Sona Vasudevan; Yanli Wang; Roxanne A Yamashita; Jodie J Yin; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

2.  The EMBL Nucleotide Sequence Database: major new developments.

Authors:  Guenter Stoesser; Wendy Baker; Alexandra van den Broek; Maria Garcia-Pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Francesco Nardone; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

3.  GenBank.

Authors:  Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; David L Wheeler
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  DNA Data Bank of Japan (DDBJ) for genome scale research in life science.

Authors:  Y Tateno; T Imanishi; S Miyazaki; K Fukami-Kobayashi; N Saitou; H Sugawara; T Gojobori
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  Database divisions and homology search files: a guide for the perplexed.

Authors:  B F Ouellette; M S Boguski
Journal:  Genome Res       Date:  1997-10       Impact factor: 9.043

Review 6.  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

7.  dbEST--database for "expressed sequence tags".

Authors:  M S Boguski; T M Lowe; C M Tolstoshev
Journal:  Nat Genet       Date:  1993-08       Impact factor: 38.330

8.  Genomic sequence sampling: a strategy for high resolution sequence-based physical mapping of complex genomes.

Authors:  M W Smith; A L Holmsen; Y H Wei; M Peterson; G A Evans
Journal:  Nat Genet       Date:  1994-05       Impact factor: 38.330

9.  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

10.  Database resources of the National Center for Biotechnology.

Authors:  David L Wheeler; Deanna M Church; Scott Federhen; Alex E Lash; Thomas L Madden; Joan U Pontius; Gregory D Schuler; Lynn M Schriml; Edwin Sequeira; Tatiana A Tatusova; Lukas Wagner
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

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  192 in total

1.  Combined proteomic and molecular approaches for cloning and characterization of copper-zinc superoxide dismutase (Cu, Zn-SOD2) from garlic (Allium sativum).

Authors:  Imen Hadji Sfaxi; Aymen Ezzine; Laurent Coquet; Pascal Cosette; Thierry Jouenne; M Nejib Marzouki
Journal:  Mol Biotechnol       Date:  2012-09       Impact factor: 2.695

2.  CysView: protein classification based on cysteine pairing patterns.

Authors:  Johann Lenffer; Paulo Lai; Wafaa El Mejaber; Asif M Khan; Judice L Y Koh; Paul T J Tan; Seng H Seah; Vladimir Brusic
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

3.  IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis.

Authors:  Véronique Giudicelli; Denys Chaume; Marie-Paule Lefranc
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

4.  PDA: a pipeline to explore and estimate polymorphism in large DNA databases.

Authors:  Sònia Casillas; Antonio Barbadilla
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

5.  Proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison.

Authors:  Masafumi Arai; Kosuke Okumura; Masanobu Satake; Toshio Shimizu
Journal:  Protein Sci       Date:  2004-08       Impact factor: 6.725

6.  Novel protein genes in animal mtDNA: a new sex determination system in freshwater mussels (Bivalvia: Unionoida)?

Authors:  Sophie Breton; Donald T Stewart; Sally Shepardson; Richard J Trdan; Arthur E Bogan; Eric G Chapman; Andrew J Ruminas; Helen Piontkivska; Walter R Hoeh
Journal:  Mol Biol Evol       Date:  2010-12-20       Impact factor: 16.240

Review 7.  Ferlins: regulators of vesicle fusion for auditory neurotransmission, receptor trafficking and membrane repair.

Authors:  Angela Lek; Frances J Evesson; R Bryan Sutton; Kathryn N North; Sandra T Cooper
Journal:  Traffic       Date:  2011-09-06       Impact factor: 6.215

8.  Selection of early-occurring mutations dictates hormone-independent progression in mouse mammary tumor lines.

Authors:  Albana Gattelli; María N Zimberlin; Roberto P Meiss; Lucio H Castilla; Edith C Kordon
Journal:  J Virol       Date:  2006-09-13       Impact factor: 5.103

9.  Gene and alternative splicing annotation with AIR.

Authors:  Liliana Florea; Valentina Di Francesco; Jason Miller; Russell Turner; Alison Yao; Michael Harris; Brian Walenz; Clark Mobarry; Gennady V Merkulov; Rosane Charlab; Ian Dew; Zuoming Deng; Sorin Istrail; Peter Li; Granger Sutton
Journal:  Genome Res       Date:  2005-01       Impact factor: 9.043

10.  Role of bacterial adhesion in the microbial ecology of biofilms in cooling tower systems.

Authors:  Yang Liu; Wei Zhang; Tadas Sileika; Richard Warta; Nicholas P Cianciotto; Aaron Packman
Journal:  Biofouling       Date:  2009       Impact factor: 3.209

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