Literature DB >> 11752243

GenBank.

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

Abstract

The GenBank sequence database incorporates publicly available DNA sequences of more than 105 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated 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 literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of World Wide Web retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov.

Mesh:

Year:  2002        PMID: 11752243      PMCID: PMC99127          DOI: 10.1093/nar/30.1.17

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


  13 in total

1.  DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams.

Authors:  Y Tateno; S Miyazaki; M Ota; H Sugawara; T Gojobori
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  GenBank.

Authors:  D A Benson; I Karsch-Mizrachi; D J Lipman; J Ostell; B A Rapp; D L Wheeler
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  The EMBL nucleotide sequence database.

Authors:  G Stoesser; W Baker; A van den Broek; E Camon; M Garcia-Pastor; C Kanz; T Kulikova; V Lombard; R Lopez; H Parkinson; N Redaschi; P Sterk; P Stoehr; M A Tuli
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

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

Authors:  Yanli Wang; John B Anderson; Jie Chen; Lewis Y Geer; Siqian He; David I Hurwitz; Cynthia A Liebert; Thomas Madej; Gabriele H Marchler; Aron Marchler-Bauer; Anna R Panchenko; Benjamin A Shoemaker; James S Song; Paul A Thiessen; Roxanne A Yamashita; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

Review 5.  Pieces of the puzzle: expressed sequence tags and the catalog of human genes.

Authors:  G D Schuler
Journal:  J Mol Med (Berl)       Date:  1997-10       Impact factor: 4.599

6.  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 7.  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

8.  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

9.  An STS-based map of the human genome.

Authors:  T J Hudson; L D Stein; S S Gerety; J Ma; A B Castle; J Silva; D K Slonim; R Baptista; L Kruglyak; S H Xu; X Hu; A M Colbert; C Rosenberg; M P Reeve-Daly; S Rozen; L Hui; X Wu; C Vestergaard; K M Wilson; J S Bae; S Maitra; S Ganiatsas; C A Evans; M M DeAngelis; K A Ingalls; R W Nahf; L T Horton; M O Anderson; A J Collymore; W Ye; V Kouyoumjian; I S Zemsteva; J Tam; R Devine; D F Courtney; M T Renaud; H Nguyen; T J O'Connor; C Fizames; S Fauré; G Gyapay; C Dib; J Morissette; J B Orlin; B W Birren; N Goodman; J Weissenbach; T L Hawkins; S Foote; D C Page; E S Lander
Journal:  Science       Date:  1995-12-22       Impact factor: 47.728

10.  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

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  134 in total

1.  LIGAND: database of chemical compounds and reactions in biological pathways.

Authors:  Susumu Goto; Yasushi Okuno; Masahiro Hattori; Takaaki Nishioka; Minoru Kanehisa
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.

Authors:  Gregory L Moore; Costas D Maranas
Journal:  Nucleic Acids Res       Date:  2002-06-01       Impact factor: 16.971

Review 3.  The challenges of recording phenotype in a generalizable and computable form.

Authors:  P M Nadkarni
Journal:  Pharmacogenomics J       Date:  2003       Impact factor: 3.550

4.  Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.

Authors:  Morten Nielsen; Claus Lundegaard; Peder Worning; Sanne Lise Lauemøller; Kasper Lamberth; Søren Buus; Søren Brunak; Ole Lund
Journal:  Protein Sci       Date:  2003-05       Impact factor: 6.725

5.  16S ribosomal DNA sequence-based analysis of clinically significant gram-positive anaerobic cocci.

Authors:  Yuli Song; Chengxu Liu; Maureen McTeague; Sydney M Finegold
Journal:  J Clin Microbiol       Date:  2003-04       Impact factor: 5.948

6.  The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds.

Authors:  Parag Mallick; Robert Weiss; David Eisenberg
Journal:  Proc Natl Acad Sci U S A       Date:  2002-12-02       Impact factor: 11.205

7.  Characterization of SDS-degrading Delftia acidovorans and in situ monitoring of its temporal succession in SDS-contaminated surface waters.

Authors:  Fadime Yilmaz; Bulent Icgen
Journal:  Environ Sci Pollut Res Int       Date:  2014-03-04       Impact factor: 4.223

8.  Dietary zinc modulates gene expression in murine thymus: results from a comprehensive differential display screening.

Authors:  J Bernadette Moore; Raymond K Blanchard; Robert J Cousins
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-19       Impact factor: 11.205

9.  Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.

Authors:  Terrence S Furey; Mark Diekhans; Yontao Lu; Tina A Graves; Lachlan Oddy; Jennifer Randall-Maher; LaDeana W Hillier; Richard K Wilson; David Haussler
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

10.  Rapid propagation of norovirus gastrointestinal illness through multiple nursing homes following a pilgrimage.

Authors:  R Fretz; H Schmid; U Kayser; P Svoboda; M Tanner; A Baumgartner
Journal:  Eur J Clin Microbiol Infect Dis       Date:  2003-09-27       Impact factor: 3.267

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