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Nucleic Acids Research, 2003, Vol. 31, No. 1 28-33
© 2003 Oxford University Press

Database resources of the National Center for Biotechnology

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 and Lukas Wagner

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 3014962475/+1 3014355950; Fax: +1 3014809241; Email: wheeler{at}ncbi.nlm.nih.gov

ABSTRACT

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, 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 data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.


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M. L. Kelley, K. E. Keiger, C. J. Lee, and J. M. Huibregtse
The Global Transcriptional Effects of the Human Papillomavirus E6 Protein in Cervical Carcinoma Cell Lines Are Mediated by the E6AP Ubiquitin Ligase
J. Virol., March 15, 2005; 79(6): 3737 - 3747.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
Y. Huang, J. Pumphrey, and A. R. Gingle
ESTminer: a Web interface for mining EST contig and cluster databases
Bioinformatics, March 1, 2005; 21(5): 669 - 670.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
I. Yanai, H. Benjamin, M. Shmoish, V. Chalifa-Caspi, M. Shklar, R. Ophir, A. Bar-Even, S. Horn-Saban, M. Safran, E. Domany, et al.
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
Bioinformatics, March 1, 2005; 21(5): 650 - 659.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
S. Olivari, C. Galli, H. Alanen, L. Ruddock, and M. Molinari
A Novel Stress-induced EDEM Variant Regulating Endoplasmic Reticulum-associated Glycoprotein Degradation
J. Biol. Chem., January 28, 2005; 280(4): 2424 - 2428.
[Abstract] [Full Text] [PDF]

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 DNA ResHome page
N. Okazaki, K. Imai, R. F. Kikuno, K. Misawa, M. Kawai, S. Inamoto, R. Ohara, T. Nagase, O. Ohara, and H. Koga
Influence of the 3'-UTR-length of mKIAA cDNAs and their Sequence Features to the mRNA Expression Level in the Brain
DNA Res, January 1, 2005; 12(3): 181 - 189.
[Abstract] [Full Text] [PDF]

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 Crop Sci.Home page
M. Luo, P. Dang, B. Z. Guo, G. He, C. C. Holbrook, M. G. Bausher, and R. D. Lee
Generation of Expressed Sequence Tags (ESTs) for Gene Discovery and Marker Development in Cultivated Peanut
Crop Sci., January 1, 2005; 45(1): 346 - 353.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
V. D. Marinescu, I. S. Kohane, and A. Riva
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D91 - D97.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
H. Zhang, J. Hu, M. Recce, and B. Tian
PolyA_DB: a database for mammalian mRNA polyadenylation
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D116 - D120.
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 Nucleic Acids ResHome page
E. J. Lefkowitz, C. Upton, S. S. Changayil, C. Buck, P. Traktman, and R. M. L. Buller
Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D311 - D316.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
Y. Kasai, S.-i. Hashimoto, T. Yamada, J. Sese, S. Sugano, K. Matsushima, and S. Morishita
5'SAGE: 5'-end Serial Analysis of Gene Expression database
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D550 - D552.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
M. Tanino, M.-A. Debily, T. Tamura, T. Hishiki, O. Ogasawara, K. Murakawa, S. Kawamoto, K. Itoh, S. Watanabe, S. J. de Souza, et al.
The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D567 - D572.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
S. Rudd
openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D622 - D627.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
Y. He, R. R. Vines, A. R. Wattam, G. V. Abramochkin, A. W. Dickerman, J. D. Eckart, and B. W. S. Sobral
PIML: the Pathogen Information Markup Language
Bioinformatics, January 1, 2005; 21(1): 116 - 121.
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 J. Biol. Chem.Home page
A. X. Tran, M. J. Karbarz, X. Wang, C. R. H. Raetz, S. C. McGrath, R. J. Cotter, and M. S. Trent
Periplasmic Cleavage and Modification of the 1-Phosphate Group of Helicobacter pylori Lipid A
J. Biol. Chem., December 31, 2004; 279(53): 55780 - 55791.
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 ScienceHome page
P. Bertone, V. Stolc, T. E. Royce, J. S. Rozowsky, A. E. Urban, X. Zhu, J. L. Rinn, W. Tongprasit, M. Samanta, S. Weissman, et al.
Global Identification of Human Transcribed Sequences with Genome Tiling Arrays
Science, December 24, 2004; 306(5705): 2242 - 2246.
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 J. Biol. Chem.Home page
X. Wang, M. J. Karbarz, S. C. McGrath, R. J. Cotter, and C. R. H. Raetz
MsbA Transporter-dependent Lipid A 1-Dephosphorylation on the Periplasmic Surface of the Inner Membrane: TOPOGRAPHY OF FRANCISELLA NOVICIDA LpxE EXPRESSED IN ESCHERICHIA COLI
J. Biol. Chem., November 19, 2004; 279(47): 49470 - 49478.
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 Nucleic Acids ResHome page
A. Metsis, U. Andersson, G. Bauren, P. Ernfors, P. Lonnerberg, A. Montelius, M. Oldin, A. Pihlak, and S. Linnarsson
Whole-genome expression profiling through fragment display and combinatorial gene identification
Nucleic Acids Res., September 8, 2004; 32(16): e127 - e127.
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 Hum Mol GenetHome page
P. N. Robinson, U. Bohme, R. Lopez, S. Mundlos, and P. Nurnberg
Gene-Ontology analysis reveals association of tissue-specific 5' CpG-island genes with development and embryogenesis
Hum. Mol. Genet., September 1, 2004; 13(17): 1969 - 1978.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
J. Leipzig, P. Pevzner, and S. Heber
The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome
Nucleic Acids Res., August 3, 2004; 32(13): 3977 - 3983.
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 J. Virol.Home page
Y. Bao, S. Federhen, D. Leipe, V. Pham, S. Resenchuk, M. Rozanov, R. Tatusov, and T. Tatusova
National Center for Biotechnology Information Viral Genomes Project
J. Virol., July 15, 2004; 78(14): 7291 - 7298.
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 J. Virol.Home page
A. Garcia-Maruniak, J. E. Maruniak, P. M. A. Zanotto, A. E. Doumbouya, J.-C. Liu, T. M. Merritt, and J. S. Lanoie
Sequence Analysis of the Genome of the Neodiprion sertifer Nucleopolyhedrovirus
J. Virol., July 1, 2004; 78(13): 7036 - 7051.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
Y. Naito, T. Yamada, K. Ui-Tei, S. Morishita, and K. Saigo
siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W124 - W129.
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 Nucleic Acids ResHome page
A. S. Halees and Z. Weng
PromoSer: improvements to the algorithm, visualization and accessibility
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W191 - W194.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
C. Muller, M. Denis, L. Gentzbittel, and T. Faraut
The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W429 - W434.
[Abstract] [Full Text] [PDF]

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 Mol. Biol. CellHome page
R. Bauer, C. Lehmann, J. Martini, F. Eckardt, and M. Hoch
Gap Junction Channel Protein Innexin 2 Is Essential for Epithelial Morphogenesis in the Drosophila Embryo
Mol. Biol. Cell, June 1, 2004; 15(6): 2992 - 3004.
[Abstract] [Full Text] [PDF]


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