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Nucleic Acids Research 2005 33(Database Issue):D39-D45; doi:10.1093/nar/gki062
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Nucleic Acids Research, 2005, Vol. 33, Database issue D39-D45
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

Database resources of the National Center for Biotechnology Information

David L. Wheeler*, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Wolfgang Helmberg, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Joan U. Pontius, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Grigory Starchenko, Tugba O. Suzek, Roman Tatusov, Tatiana A. Tatusova, Lukas Wagner and Eugene Yaschenko

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA

* To whom correspondence should be addressed. Tel: +1 301 435 5950; Fax: +1 301 480 9241; Email: wheeler{at}ncbi.nlm.nih.gov

Received September 15, 2004; Revised and Accepted October 5, 2004

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data retrieval systems and computational resources for the analysis of data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, Entrez Programming Utilities, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.


The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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Nucleic Acids ResHome page
F. Pattyn, P. Robbrecht, A. De Paepe, F. Speleman, and J. Vandesompele
RTPrimerDB: the real-time PCR primer and probe database, major update 2006
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D684 - D688.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
S. Hartmann, D. Lu, J. Phillips, and T. J. Vision
Phytome: a platform for plant comparative genomics
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D724 - D730.
[Abstract] [Full Text] [PDF]


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BioinformaticsHome page
H. Liu, Z.-Z. Hu, J. Zhang, and C. Wu
BioThesaurus: a web-based thesaurus of protein and gene names
Bioinformatics, January 1, 2006; 22(1): 103 - 105.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
L. L. Elo, L. Lahti, H. Skottman, M. Kylaniemi, R. Lahesmaa, and T. Aittokallio
Integrating probe-level expression changes across generations of Affymetrix arrays
Nucleic Acids Res., December 14, 2005; 33(22): e193 - e193.
[Abstract] [Full Text] [PDF]


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Genome ResHome page
P. F.R. Little
Structure and function of the human genome
Genome Res., December 1, 2005; 15(12): 1759 - 1766.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
A. Fadiel, I. Anidi, and K. D. Eichenbaum
Farm animal genomics and informatics: an update
Nucleic Acids Res., November 7, 2005; 33(19): 6308 - 6318.
[Abstract] [Full Text] [PDF]


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Cancer Epidemiol. Biomarkers Prev.Home page
M. F. Rudd, R. D. Williams, E. L. Webb, S. Schmidt, G. S. Sellick, and R. S. Houlston
The Predicted Impact of Coding Single Nucleotide Polymorphisms Database
Cancer Epidemiol. Biomarkers Prev., November 1, 2005; 14(11): 2598 - 2604.
[Abstract] [Full Text] [PDF]


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Cancer Res.Home page
D. J. Samuelson, B. A. Aperavich, J. D. Haag, and M. N. Gould
Fine Mapping Reveals Multiple Loci and a Possible Epistatic Interaction within the Mammary Carcinoma Susceptibility Quantitative Trait Locus, Mcs5
Cancer Res., November 1, 2005; 65(21): 9637 - 9642.
[Abstract] [Full Text] [PDF]


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Genome ResHome page
G. A. Thorisson, A. V. Smith, L. Krishnan, and L. D. Stein
The International HapMap Project Web site
Genome Res., November 1, 2005; 15(11): 1592 - 1593.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
T. Watanabe, J. O. Blaisdell, S. S. Wallace, and J. P. Bond
Engineering Functional Changes in Escherichia coli Endonuclease III Based on Phylogenetic and Structural Analyses
J. Biol. Chem., October 7, 2005; 280(40): 34378 - 34384.
[Abstract] [Full Text] [PDF]


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Genome ResHome page
B. Giardine, C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski, P. Shah, Y. Zhang, D. Blankenberg, I. Albert, J. Taylor, et al.
Galaxy: A platform for interactive large-scale genome analysis
Genome Res., October 1, 2005; 15(10): 1451 - 1455.
[Abstract] [Full Text] [PDF]


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J. Biol. Chem.Home page
D. Mokranjac, M. Sichting, D. Popov-Celeketic, A. Berg, K. Hell, and W. Neupert
The Import Motor of the Yeast Mitochondrial TIM23 Preprotein Translocase Contains Two Different J Proteins, Tim14 and Mdj2
J. Biol. Chem., September 9, 2005; 280(36): 31608 - 31614.
[Abstract] [Full Text] [PDF]


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J. Clin. Microbiol.Home page
M. Drancourt and D. Raoult
Sequence-Based Identification of New Bacteria: a Proposition for Creation of an Orphan Bacterium Repository
J. Clin. Microbiol., September 1, 2005; 43(9): 4311 - 4315.
[Full Text] [PDF]


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Phil Trans R Soc BHome page
H. F Willard, M. Angrist, and G. S Ginsburg
Genomic medicine: genetic variation and its impact on the future of health care
Phil Trans R Soc B, August 29, 2005; 360(1460): 1543 - 1550.
[Abstract] [Full Text] [PDF]


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Hum Mol GenetHome page
F. A. Kondrashov
Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
Hum. Mol. Genet., August 15, 2005; 14(16): 2415 - 2419.
[Abstract] [Full Text] [PDF]


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BioinformaticsHome page
M. Smith, V. Kunin, L. Goldovsky, A. J. Enright, and C. A. Ouzounis
MagicMatch--cross-referencing sequence identifiers across databases
Bioinformatics, August 15, 2005; 21(16): 3429 - 3430.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
P. Piccinelli, M. A. Rosenblad, and T. Samuelsson
Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes
Nucleic Acids Res., August 8, 2005; 33(14): 4485 - 4495.
[Abstract] [Full Text] [PDF]


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MicrobiologyHome page
D. Field, E. J. Feil, and G. A. Wilson
Databases and software for the comparison of prokaryotic genomes
Microbiology, July 1, 2005; 151(7): 2125 - 2132.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
G. G. Loots and I. Ovcharenko
Dcode.org anthology of comparative genomic tools
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W56 - W64.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
D. L. Corcoran, E. Feingold, and P. V. Benos
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W442 - W446.
[Abstract] [Full Text] [PDF]


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Nucleic Acids ResHome page
H. Maier, S. Dohr, K. Grote, S. O'Keeffe, T. Werner, M. H. de Angelis, and R. Schneider
LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W779 - W782.
[Abstract] [Full Text] [PDF]


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Plant Physiol.Home page
D. L. Wheeler, B. Smith-White, V. Chetvernin, S. Resenchuk, S. M. Dombrowski, S. W. Pechous, T. Tatusova, and J. Ostell
Plant Genome Resources at the National Center for Biotechnology Information
Plant Physiology, July 1, 2005; 138(3): 1280 - 1288.
[Abstract] [Full Text] [PDF]


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Sci SignalHome page
E. Neumann
A Life Science Semantic Web: Are We There Yet?
Sci. Signal., May 10, 2005; 2005(283): pe22 - pe22.
[Abstract] [Full Text] [PDF]


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aacredbookHome page
W. C. Lathe, M. E. Mangan, D. Karolchik, W. J. Kent, and D. Haussler
Integrating Genomic Information through the UCSC Genome Browser
Am. Assoc. Cancer Res. Educ. Book, April 1, 2005; 2005(1): 3 - 6.
[Full Text] [PDF]


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Nucleic Acids ResHome page
D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler
GenBank
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D34 - D38.
[Abstract] [Full Text] [PDF]



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