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PMID: 23193264 Published · ppublish English Journal Article Research Support, N.I.H., Intramural

Database resources of the National Center for Biotechnology Information.

Nucleic acids research ·Vol. 41 ·No. Database issue ·2013-01-00 ·Pages D8-D20

NCBI Resource Coordinators

Abstract

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page.

MeSH Terms
Animals Databases, Chemical Databases, Genetic Databases, Nucleic Acid Databases, Protein Disease/genetics Gene Expression Genetic Testing Genomics Humans Internet National Library of Medicine (U.S.) Protein Structure, Tertiary PubMed Registries Sequence Alignment United States
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
NCBI Resource Coordinators
Investigators
60 investigators, click to expand
Acland Abigail
Agarwala Richa
Barrett Tanya
Beck Jeff
Benson Dennis A
Bollin Colleen
Bolton Evan
Bryant Stephen H
Canese Kathi
Church Deanna M
Clark Karen
DiCuccio Michael
Dondoshansky Ilya
Federhen Scott
Feolo Michael
Geer Lewis Y
Gorelenkov Viatcheslav
Hoeppner Marilu
Johnson Mark
Kelly Christopher
Khotomlianski Viatcheslav
Kimchi Avi
Kimelman Michael
Kitts Paul
Krasnov Sergey
Kuznetsov Anatoliy
Landsman David
Lipman David J
Lu Zhiyong
Madden Thomas L
Madej Tom
Maglott Donna R
Marchler-Bauer Aron
Karsch-Mizrachi Ilene
Murphy Terence
Ostell James
O'Sullivan Christopher
Panchenko Anna
Phan Lon
Pruitt Don Preussm Kim D
Rubinstein Wendy
Sayers Eric W
Schneider Valerie
Schuler Gregory D
Sequeira Edwin
Sherry Stephen T
Shumway Martin
Sirotkin Karl
Siyan Karanjit
Slotta Douglas
Soboleva Alexandra
Starchenko Grigory
Tatusova Tatiana A
Trawick Bart
Vakatov Denis
Wang Yanli
Ward Minghong
Wilbur W John
Yaschenko Eugene
Zbicz Kerry
References (63)
63 references, click to expand
  1. The mouse genome database (MGD): new features facilitating a model system.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D630-7 PMID: 17135206
  2. Primer3 on the WWW for general users and for biologist programmers.
    Methods Mol Biol. 2000;132:365-86 PMID: 10547847
  3. MMDB: 3D structures and macromolecular interactions.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D461-4 PMID: 22135289
  4. PatternHunter: faster and more sensitive homology search.
    Bioinformatics. 2002 Mar;18(3):440-5 PMID: 11934743
  5. BLAST: improvements for better sequence analysis.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W6-9 PMID: 16845079
  6. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.
    Nature. 2005 Oct 20;437(7062):1162-6 PMID: 16208317
  7. Domain enhanced lookup time accelerated BLAST.
    Biol Direct. 2012 Apr 17;7:12 PMID: 22510480
  8. New models of collaboration in genome-wide association studies: the Genetic Association Information Network.
    Nat Genet. 2007 Sep;39(9):1045-51 PMID: 17728769
  9. PubChem's BioAssay Database.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D400-12 PMID: 22140110
  10. OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D599-601 PMID: 16381939
  11. The Zebrafish Information Network: the zebrafish model organism database.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D581-5 PMID: 16381936
  12. The Sequence Read Archive: explosive growth of sequencing data.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D54-6 PMID: 22009675
  13. Threading a database of protein cores.
    Proteins. 1995 Nov;23(3):356-69 PMID: 8710828
  14. Clinical laboratory reports in molecular pathology.
    Arch Pathol Lab Med. 2007 Jun;131(6):852-63 PMID: 17550311
  15. dbSNP: the NCBI database of genetic variation.
    Nucleic Acids Res. 2001 Jan 1;29(1):308-11 PMID: 11125122
  16. GenBank.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D48-53 PMID: 22144687
  17. Allelic genes of blood group antigens: a source of human mutations and cSNPs documented in the Blood Group Antigen Gene Mutation Database.
    Hum Mutat. 2004 Jan;23(1):8-16 PMID: 14695527
  18. Entrez: molecular biology database and retrieval system.
    Methods Enzymol. 1996;266:141-62 PMID: 8743683
  19. From genomics to chemical genomics: new developments in KEGG.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7 PMID: 16381885
  20. CDD: a Conserved Domain Database for the functional annotation of proteins.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9 PMID: 21109532
  21. NCBI Reference Sequences: current status, policy and new initiatives.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D32-6 PMID: 18927115
  22. Cn3D: sequence and structure views for Entrez.
    Trends Biochem Sci. 2000 Jun;25(6):300-2 PMID: 10838572
  23. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
    Genome Res. 2009 Jul;19(7):1316-23 PMID: 19498102
  24. The NCBI Taxonomy database.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D136-43 PMID: 22139910
  25. MEDICAL SUBJECT HEADINGS IN MEDLARS.
    Bull Med Libr Assoc. 1964 Jan;52:164-70 PMID: 14119288
  26. Entrez Gene: gene-centered information at NCBI.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D52-7 PMID: 21115458
  27. EcoCyc: a comprehensive view of Escherichia coli biology.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D464-70 PMID: 18974181
  28. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  29. McKusick's Online Mendelian Inheritance in Man (OMIM).
    Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6 PMID: 18842627
  30. CDD: specific functional annotation with the Conserved Domain Database.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D205-10 PMID: 18984618
  31. NCBI Epigenomics: a new public resource for exploring epigenomic data sets.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D908-12 PMID: 21075792
  32. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5 PMID: 22121212
  33. Mining biological pathways using WikiPathways web services.
    PLoS One. 2009 Jul 30;4(7):e6447 PMID: 19649250
  34. WikiPathways: pathway editing for the people.
    PLoS Biol. 2008 Jul 22;6(7):e184 PMID: 18651794
  35. The National Center for Biotechnology Information's Protein Clusters Database.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D216-23 PMID: 18940865
  36. Human immunodeficiency virus type 1, human protein interaction database at NCBI.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D417-22 PMID: 18927109
  37. Gene Ontology annotations at SGD: new data sources and annotation methods.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81 PMID: 17982175
  38. SMART 5: domains in the context of genomes and networks.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D257-60 PMID: 16381859
  39. NCBI GEO: archive for functional genomics data sets--update.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5 PMID: 23193258
  40. PubChem: a public information system for analyzing bioactivities of small molecules.
    Nucleic Acids Res. 2009 Jul;37(Web Server issue):W623-33 PMID: 19498078
  41. GeneTests: an online genetic information resource for health care providers.
    J Med Libr Assoc. 2006 Jul;94(3):343-8 PMID: 16888670
  42. Pfam: clans, web tools and services.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51 PMID: 16381856
  43. PID: the Pathway Interaction Database.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D674-9 PMID: 18832364
  44. UniProt Knowledgebase: a hub of integrated protein data.
    Database (Oxford). 2011 Mar 29;2011:bar009 PMID: 21447597
  45. The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences.
    Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W173-5 PMID: 15215374
  46. Clone DB: an integrated NCBI resource for clone-associated data.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D1070-8 PMID: 23193260
  47. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D301-3 PMID: 17142228
  48. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  49. COBALT: constraint-based alignment tool for multiple protein sequences.
    Bioinformatics. 2007 May 1;23(9):1073-9 PMID: 17332019
  50. The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D925-35 PMID: 23193275
  51. A greedy algorithm for aligning DNA sequences.
    J Comput Biol. 2000 Feb-Apr;7(1-2):203-14 PMID: 10890397
  52. KEGG for linking genomes to life and the environment.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4 PMID: 18077471
  53. Diversity of human copy number variation and multicopy genes.
    Science. 2010 Oct 29;330(6004):641-6 PMID: 21030649
  54. KEGG: kyoto encyclopedia of genes and genomes.
    Nucleic Acids Res. 2000 Jan 1;28(1):27-30 PMID: 10592173
  55. BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D57-63 PMID: 22139929
  56. Reactome knowledgebase of human biological pathways and processes.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22 PMID: 18981052
  57. FlyBase: genomes by the dozen.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D486-91 PMID: 17099233
  58. Pieces of the puzzle: expressed sequence tags and the catalog of human genes.
    J Mol Med (Berl). 1997 Oct;75(10):694-8 PMID: 9382993
  59. Public data archives for genomic structural variation.
    Nat Genet. 2010 Oct;42(10):813-4 PMID: 20877315
  60. Surprising similarities in structure comparison.
    Curr Opin Struct Biol. 1996 Jun;6(3):377-85 PMID: 8804824
  61. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  62. The TIGRFAMs database of protein families.
    Nucleic Acids Res. 2003 Jan 1;31(1):371-3 PMID: 12520025
  63. Internet resources in medical genetics.
    Curr Protoc Hum Genet. 2009 Jul;Chapter 9:Unit 9.12 PMID: 19582767
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
Published
2013-01-00
Epub
2012-00-27
Pages
D8-D20
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3531099
Subset
IM
Grants
Intramural NIH HHS · United States
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