Nucleic Acids Research Advance Access originally published online on November 27, 2007
Nucleic Acids Research 2008 36(Database issue):D13-D21; doi:10.1093/nar/gkm1000
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, Database issue D13-D21
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
Database resources of the National Center for Biotechnology Information
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: +1 301 496 2475; Fax: +1 301 480 9241; Email: wheeler{at}ncbi.nlm.nih.gov
Received September 18, 2007. Revised October 19, 2007. Accepted October 22, 2007.
In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. M. Hettne, R. H. Stierum, M. J. Schuemie, P. J. M. Hendriksen, B. J. A. Schijvenaars, E. M. v. Mulligen, J. Kleinjans, and J. A. Kors A dictionary to identify small molecules and drugs in free text Bioinformatics, November 15, 2009; 25(22): 2983 - 2991. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Genome 10K Community of Scientists Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species J. Hered., November 6, 2009; (2009) esp086v2. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. S. Barker, H. Vogel, and M. E. Schranz Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales Gen Biol Evol, November 3, 2009; 2009(0): 391 - 399. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. D. Rawlings A large and accurate collection of peptidase cleavages in the MEROPS database Database, November 2, 2009; 2009(0): bap015 - bap015. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Valdivia-Granda and F. Larson ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies Database, October 12, 2009; 2009(0): bap014 - bap014. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Rastgou, M. K. Habibi, K. Izadpanah, V. Masenga, R. G. Milne, Y. I. Wolf, E. V. Koonin, and M. Turina Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin J. Gen. Virol., October 1, 2009; 90(10): 2525 - 2535. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. R.M. Tillier and R. L. Charlebois The human protein coevolution network Genome Res., October 1, 2009; 19(10): 1861 - 1871. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Jimenez-Lozano, J. Segura, J. R. Macias, J. Vega, and J. M. Carazo aGEM: an integrative system for analyzing spatial-temporal gene-expression information Bioinformatics, October 1, 2009; 25(19): 2566 - 2572. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. T. Lee Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome Genes & Dev., August 15, 2009; 23(16): 1831 - 1842. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Carter, S. Chen, L. Isik, S. Tyekucheva, V. E. Velculescu, K. W. Kinzler, B. Vogelstein, and R. Karchin Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations Cancer Res., August 15, 2009; 69(16): 6660 - 6667. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. Lawson and L. Zhang Sexy gene conversions: locating gene conversions on the X-chromosome Nucleic Acids Res., August 1, 2009; 37(14): 4570 - 4579. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Zhu, J. Zeng, and H. Mamitsuka Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity Bioinformatics, August 1, 2009; 25(15): 1944 - 1951. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. J. Taft, E. A. Glazov, T. Lassmann, Y. Hayashizaki, P. Carninci, and J. S. Mattick Small RNAs derived from snoRNAs RNA, July 1, 2009; 15(7): 1233 - 1240. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. D. Pruitt, J. Harrow, R. A. Harte, C. Wallin, M. Diekhans, D. R. Maglott, S. Searle, C. M. Farrell, J. E. Loveland, B. J. Ruef, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes Genome Res., July 1, 2009; 19(7): 1316 - 1323. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kuzniar, K. Lin, Y. He, H. Nijveen, S. Pongor, and J. A. M. Leunissen ProGMap: an integrated annotation resource for protein orthology Nucleic Acids Res., July 1, 2009; 37(suppl_2): W428 - W434. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Joseph and D. Durand Family classification without domain chaining Bioinformatics, June 15, 2009; 25(12): i45 - i53. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Zhou, M. Pertea, A. L. Delcher, and L. Florea Sim4cc: a cross-species spliced alignment program Nucleic Acids Res., June 1, 2009; 37(11): e80 - e80. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. R. Williams-Devane, M. A. Wolf, and A. M. Richard Toward a Public Toxicogenomics Capability for Supporting Predictive Toxicology: Survey of Current Resources and Chemical Indexing of Experiments in GEO and ArrayExpress Toxicol. Sci., June 1, 2009; 109(2): 358 - 371. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Spasic, E. Simeonidis, H. L. Messiha, N. W. Paton, and D. B. Kell KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways Bioinformatics, June 1, 2009; 25(11): 1404 - 1411. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. C. Daniel, L. Marchionni, J. S. Hierman, J. T. Rhodes, W. L. Devereux, C. M. Rudin, R. Yung, G. Parmigiani, M. Dorsch, C. D. Peacock, et al. A Primary Xenograft Model of Small-Cell Lung Cancer Reveals Irreversible Changes in Gene Expression Imposed by Culture In vitro Cancer Res., April 15, 2009; 69(8): 3364 - 3373. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Wang and T. S. Furey Analysis of Complex Disease Association and Linkage Studies Using the University of California Santa Cruz Genome Browser Circ Cardiovasc Genet, April 1, 2009; 2(2): 199 - 204. [Full Text] [PDF]
|
|
|
|
|
|
J. P. de Magalhaes, J. Curado, and G. M. Church Meta-analysis of age-related gene expression profiles identifies common signatures of aging Bioinformatics, April 1, 2009; 25(7): 875 - 881. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Dumontier and N. Villanueva-Rosales Towards pharmacogenomics knowledge discovery with the semantic web Brief Bioinform, March 1, 2009; 10(2): 153 - 163. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. F. Altschul, E. M. Gertz, R. Agarwala, A. A. Schaffer, and Y.-K. Yu PSI-BLAST pseudocounts and the minimum description length principle Nucleic Acids Res., February 1, 2009; 37(3): 815 - 824. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. V. Sharova, A. A. Sharov, T. Nedorezov, Y. Piao, N. Shaik, and M. S.H. Ko Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells DNA Res, February 1, 2009; 16(1): 45 - 58. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Vilella, J. Severin, A. Ureta-Vidal, L. Heng, R. Durbin, and E. Birney EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates Genome Res., February 1, 2009; 19(2): 327 - 335. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Taccioli, E. Fabbri, R. Visone, S. Volinia, G. A. Calin, L. Y. Fong, R. Gambari, A. Bottoni, M. Acunzo, J. Hagan, et al. UCbase & miRfunc: a database of ultraconserved sequences and microRNA function Nucleic Acids Res., January 1, 2009; 37(suppl_1): D41 - D48. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Cochrane, R. Akhtar, J. Bonfield, L. Bower, F. Demiralp, N. Faruque, R. Gibson, G. Hoad, T. Hubbard, C. Hunter, et al. Petabyte-scale innovations at the European Nucleotide Archive Nucleic Acids Res., January 1, 2009; 37(suppl_1): D19 - D25. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. L. Childs Genomic and Genetic Database Resources for the Grasses Plant Physiology, January 1, 2009; 149(1): 132 - 136. [Full Text] [PDF]
|
|
|
|
|
|
V. Quesada, G. R. Ordonez, L. M. Sanchez, X. S. Puente, and C. Lopez-Otin The Degradome database: mammalian proteases and diseases of proteolysis Nucleic Acids Res., January 1, 2009; 37(suppl_1): D239 - D243. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. P. Davis, C. G. Murphy, C. A. Saraceni-Richards, M. C. Rosenstein, T. C. Wiegers, and C. J. Mattingly Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks Nucleic Acids Res., January 1, 2009; 37(suppl_1): D786 - D792. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-Y. Li, Q.-R. Liu, P.-W. Zhang, X.-M. Li, L. Wei, and G. R. Uhl OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules Nucleic Acids Res., January 1, 2009; 37(suppl_1): D251 - D260. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. G. Almeida, N. J. Sakabe, A. R. deOliveira, M. C. C. Silva, A. S. Mundstein, T. Cohen, Y.-T. Chen, R. Chua, S. Gurung, S. Gnjatic, et al. CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens Nucleic Acids Res., January 1, 2009; 37(suppl_1): D816 - D819. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. S. Novichkov, I. Ratnere, Y. I. Wolf, E. V. Koonin, and I. Dubchak ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D448 - D454. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Klein, R. Munch, I. Biegler, I. Haddad, I. Retter, and D. Jahn Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform 'Open Genome Resource' (OGeR) Nucleic Acids Res., January 1, 2009; 37(suppl_1): D494 - D498. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Fu, B. E. Sanders-Beer, K. S. Katz, D. R. Maglott, K. D. Pruitt, and R. G. Ptak Human immunodeficiency virus type 1, human protein interaction database at NCBI Nucleic Acids Res., January 1, 2009; 37(suppl_1): D417 - D422. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Masciocchi, G. Frau, M. Fanton, M. Sturlese, M. Floris, L. Pireddu, P. Palla, F. Cedrati, P. Rodriguez-Tome, and S. Moro MMsINC: a large-scale chemoinformatics database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D284 - D290. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. C. Walter, T. Rattei, R. Arnold, U. Guldener, M. Munsterkotter, K. Nenova, G. Kastenmuller, P. Tischler, A. Wolling, A. Volz, et al. PEDANT covers all complete RefSeq genomes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D408 - D411. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Barrett, D. B. Troup, S. E. Wilhite, P. Ledoux, D. Rudnev, C. Evangelista, I. F. Kim, A. Soboleva, M. Tomashevsky, K. A. Marshall, et al. NCBI GEO: archive for high-throughput functional genomic data Nucleic Acids Res., January 1, 2009; 37(suppl_1): D885 - D890. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Pieper, N. Eswar, B. M. Webb, D. Eramian, L. Kelly, D. T. Barkan, H. Carter, P. Mankoo, R. Karchin, M. A. Marti-Renom, et al. MODBASE, a database of annotated comparative protein structure models and associated resources Nucleic Acids Res., January 1, 2009; 37(suppl_1): D347 - D354. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Harmar, R. A. Hills, E. M. Rosser, M. Jones, O. P. Buneman, D. R. Dunbar, S. D. Greenhill, V. A. Hale, J. L. Sharman, T. I. Bonner, et al. IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels Nucleic Acids Res., January 1, 2009; 37(suppl_1): D680 - D685. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. K. Shimada, R. Matsumoto, Y. Hayakawa, R. Sanbonmatsu, C. Gough, Y. Yamaguchi-Kabata, C. Yamasaki, T. Imanishi, and T. Gojobori VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts Nucleic Acids Res., January 1, 2009; 37(suppl_1): D810 - D815. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. A. O'Brien, Y. Zhang, E. Wang, V. Marie, W. Badejoko, B. F. Lang, and G. Burger GOBASE: an organelle genome database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D946 - D950. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Ding, P. Lorenz, M. Kreutzer, Y. Li, and H.-J. Thiesen SysZNF: the C2H2 zinc finger gene database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D267 - D273. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. R. Pico, I. V. Smirnov, J. S. Chang, R.-F. Yeh, J. L. Wiemels, J. K. Wiencke, T. Tihan, B. R. Conklin, and M. Wrensch SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system Nucleic Acids Res., January 1, 2009; 37(suppl_1): D803 - D809. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Chang, M. Scheer, A. Grote, I. Schomburg, and D. Schomburg BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D588 - D592. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Marchler-Bauer, J. B. Anderson, F. Chitsaz, M. K. Derbyshire, C. DeWeese-Scott, J. H. Fong, L. Y. Geer, R. C. Geer, N. R. Gonzales, M. Gwadz, et al. CDD: specific functional annotation with the Conserved Domain Database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D205 - D210. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Richardson, Q. Gao, C. Mitsopoulous, M. Zvelebil, L. H. Pearl, and F. M. G. Pearl MoKCa database--mutations of kinases in cancer Nucleic Acids Res., January 1, 2009; 37(suppl_1): D824 - D831. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. D. McDowall, M. S. Scott, and G. J. Barton PIPs: human protein-protein interaction prediction database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D651 - D656. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. S. Keshava Prasad, R. Goel, K. Kandasamy, S. Keerthikumar, S. Kumar, S. Mathivanan, D. Telikicherla, R. Raju, B. Shafreen, A. Venugopal, et al. Human Protein Reference Database--2009 update Nucleic Acids Res., January 1, 2009; 37(suppl_1): D767 - D772. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. A. Samarajiwa, S. Forster, K. Auchettl, and P. J. Hertzog INTERFEROME: the database of interferon regulated genes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D852 - D857. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Kuhn, D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, M. Pheasant, et al. The UCSC Genome Browser Database: update 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D755 - D761. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. M. Berman, J. D. Westbrook, M. J. Gabanyi, W. Tao, R. Shah, A. Kouranov, T. Schwede, K. Arnold, F. Kiefer, L. Bordoli, et al. The protein structure initiative structural genomics knowledgebase Nucleic Acids Res., January 1, 2009; 37(suppl_1): D365 - D368. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. J. P. Hubbard, B. L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, et al. Ensembl 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D690 - D697. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Kunin, A. Copeland, A. Lapidus, K. Mavromatis, and P. Hugenholtz A Bioinformatician's Guide to Metagenomics Microbiol. Mol. Biol. Rev., December 1, 2008; 72(4): 557 - 578. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Agarwal and D. B. Searls Literature mining in support of drug discovery Brief Bioinform, November 1, 2008; 9(6): 479 - 492. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. F. Berriz and F. P. Roth The Synergizer service for translating gene, protein and other biological identifiers Bioinformatics, October 1, 2008; 24(19): 2272 - 2273. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Fan, Y. Zhang, Y. Yu, S. Rounsley, M. Long, and R. A. Wing The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice Mol Plant, September 1, 2008; 1(5): 839 - 850. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Schulz, H. Stenzhorn, and M. Boeker The ontology of biological taxa Bioinformatics, July 1, 2008; 24(13): i313 - i321. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Grant and P. Stothard The CGView Server: a comparative genomics tool for circular genomes Nucleic Acids Res., July 1, 2008; 36(suppl_2): W181 - W184. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Klein, S. Leupold, R. Munch, C. Pommerenke, T. Johl, U. Karst, L. Jansch, D. Jahn, and I. Retter ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks Nucleic Acids Res., July 1, 2008; 36(suppl_2): W460 - W464. [Abstract] [Full Text] [PDF]
|
|