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
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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. Cheng, C. Knox, N. Young, P. Stothard, S. Damaraju, and D. S. Wishart PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites Nucleic Acids Res., July 1, 2008; 36(suppl_2): W399 - W405. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. U. Pontius, J. C. Mullikin, D. R. Smith, Agencourt Sequencing Team, K. Lindblad-Toh, S. Gnerre, M. Clamp, J. Chang, R. Stephens, B. Neelam, et al. Initial sequence and comparative analysis of the cat genome Genome Res., November 1, 2007; 17(11): 1675 - 1689. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Ingsriswang and E. Pacharawongsakda sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets Bioinformatics, September 15, 2007; 23(18): 2498 - 2500. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Vider-Shalit, V. Fishbain, S. Raffaeli, and Y. Louzoun Phase-Dependent Immune Evasion of Herpesviruses J. Virol., September 1, 2007; 81(17): 9536 - 9545. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Yang, D. M. Wilcox, D. L. Haasch, P. M. Jung, P. T. Nguyen, M. J. Voorbach, S. Doktor, S. Brodjian, E. N. Bush, E. Lin, et al. Liver-specific Knockdown of JNK1 Up-regulates Proliferator-activated Receptor {gamma} Coactivator 1beta and Increases Plasma Triglyceride despite Reduced Glucose and Insulin Levels in Diet-induced Obese Mice J. Biol. Chem., August 3, 2007; 282(31): 22765 - 22774. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. Wei, R. E. Davis, I.-M. Lee, and Y. Zhao Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups Int J Syst Evol Microbiol, August 1, 2007; 57(8): 1855 - 1867. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. U. Pontius and S. J. O'Brien Genome Annotation Resource Fields GARFIELD: A Genome Browser for Felis catus J. Hered., July 25, 2007; (2007) esm055v2. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. C. Fink, M. R. Evans, S. Porwollik, A. Vazquez-Torres, J. Jones-Carson, B. Troxell, S. J. Libby, M. McClelland, and H. M. Hassan FNR Is a Global Regulator of Virulence and Anaerobic Metabolism in Salmonella enterica Serovar Typhimurium (ATCC 14028s) J. Bacteriol., March 15, 2007; 189(6): 2262 - 2273. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Kim, A. Magen, and G. Ast Different levels of alternative splicing among eukaryotes Nucleic Acids Res., January 12, 2007; 35(1): 125 - 131. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhang, J. Li, L. Kong, G. Gao, Q.-R. Liu, and L. Wei NATsDB: Natural Antisense Transcripts DataBase Nucleic Acids Res., January 12, 2007; 35(suppl_1): D156 - D161. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kutchma, N. Quayum, and J. Jensen GeneSpeed: protein domain organization of the transcriptome Nucleic Acids Res., January 12, 2007; 35(suppl_1): D674 - D679. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Ren, K. Chen, and I. T. Paulsen TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels Nucleic Acids Res., January 12, 2007; 35(suppl_1): D274 - D279. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Xu, A. Canutescu, Z. Obradovic, and R. L. Dunbrack Jr ProtBuD: a database of biological unit structures of protein families and superfamilies Bioinformatics, December 1, 2006; 22(23): 2876 - 2882. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Vinogradov 'Genome design' model and multicellular complexity: golden middle Nucleic Acids Res., November 6, 2006; 34(20): 5906 - 5914. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Lenzi, F. Frabetti, F. Facchin, R. Casadei, L. Vitale, S. Canaider, P. Carinci, M. Zannotti, and P. Strippoli UniGene Tabulator: a full parser for the UniGene format Bioinformatics, October 15, 2006; 22(20): 2570 - 2571. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Gioia, X. Qin, H. Jiang, K. Clinkenbeard, R. Lo, Y. Liu, G. E. Fox, S. Yerrapragada, M. P. McLeod, T. Z. McNeill, et al. The Genome Sequence of Mannheimia haemolytica A1: Insights into Virulence, Natural Competence, and Pasteurellaceae Phylogeny. J. Bacteriol., October 1, 2006; 188(20): 7257 - 7266. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Walraven, M. A. Doll, and D. W. Hein Identification and Characterization of Functional Rat Arylamine N-Acetyltransferase 3: Comparisons with Rat Arylamine N-Acetyltransferases 1 and 2 J. Pharmacol. Exp. Ther., October 1, 2006; 319(1): 369 - 375. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Friedman, T. Borlawsky, L. Shagina, H. R. Xing, and Y. A. Lussier Bio-Ontology and text: bridging the modeling gap Bioinformatics, October 1, 2006; 22(19): 2421 - 2429. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W.-Y. Ko, S. Piao, and H. Akashi Strong Regional Heterogeneity in Base Composition Evolution on the Drosophila X Chromosome Genetics, September 1, 2006; 174(1): 349 - 362. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. R. Grimes, T. Q. Wen, M. Mewissen, R. M. Baxter, S. Moodie, J. S. Beattie, and P. Ghazal PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature Bioinformatics, August 15, 2006; 22(16): 2055 - 2057. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhang, X. S. Liu, Q.-R. Liu, and L. Wei Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species Nucleic Acids Res., July 18, 2006; 34(12): 3465 - 3475. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Penkett, J. A. Morris, V. Wood, and J. Bahler YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W330 - W334. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. M. Murphy Jr Application of microarray technology in psychotropic drug trials. J Psychopharmacol, July 1, 2006; 20(4 Suppl): 72 - 78. [Abstract] [PDF]
|
|
|
|
|
|
J. Klekota, F. P. Roth, and S. L. Schreiber Query Chem: a Google-powered web search combining text and chemical structures Bioinformatics, July 1, 2006; 22(13): 1670 - 1673. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Fire, R. Alcazar, and F. Tan Unusual DNA Structures Associated With Germline Genetic Activity in Caenorhabditis elegans Genetics, July 1, 2006; 173(3): 1259 - 1273. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Tiffin, E. Adie, F. Turner, H. G. Brunner, M. A. van Driel, M. Oti, N. Lopez-Bigas, C. Ouzounis, C. Perez-Iratxeta, M. A. Andrade-Navarro, et al. Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes Nucleic Acids Res., June 6, 2006; 34(10): 3067 - 3081. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Y. Galperin Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J. Bacteriol., June 1, 2006; 188(12): 4169 - 4182. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. L. Whetzel, H. Parkinson, H. C. Causton, L. Fan, J. Fostel, G. Fragoso, L. Game, M. Heiskanen, N. Morrison, P. Rocca-Serra, et al. The MGED Ontology: a resource for semantics-based description of microarray experiments Bioinformatics, April 1, 2006; 22(7): 866 - 873. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Schattner and M. Diekhans Regions of extreme synonymous codon selection in mammalian genes Nucleic Acids Res., March 23, 2006; 34(6): 1700 - 1710. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. P. Kastenmayer, L. Ni, A. Chu, L. E. Kitchen, W.-C. Au, H. Yang, C. D. Carter, D. Wheeler, R. W. Davis, J. D. Boeke, et al. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae. Genome Res., March 1, 2006; 16(3): 365 - 373. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. E. Vinogradov "Genome design" model: Evidence from conserved intronic sequence in human-mouse comparison Genome Res., March 1, 2006; 16(3): 347 - 354. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. B. Montgomery, O. L. Griffith, M. C. Sleumer, C. M. Bergman, M. Bilenky, E. D. Pleasance, Y. Prychyna, X. Zhang, and S. J. M. Jones ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation Bioinformatics, March 1, 2006; 22(5): 637 - 640. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Rothganger, M. Weniger, T. Weniger, A. Mellmann, and D. Harmsen Ridom TraceEdit: a DNA trace editor and viewer Bioinformatics, February 15, 2006; 22(4): 493 - 494. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Snider, I. Gutsche, M. Lin, S. Baby, B. Cox, G. Butland, J. Greenblatt, A. Emili, and W. A. Houry Formation of a Distinctive Complex between the Inducible Bacterial Lysine Decarboxylase and a Novel AAA+ ATPase J. Biol. Chem., January 20, 2006; 281(3): 1532 - 1546. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Arnold, L. Bordoli, J. Kopp, and T. Schwede The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling Bioinformatics, January 15, 2006; 22(2): 195 - 201. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Riley, T. Abe, M. B. Arnaud, M. K.B. Berlyn, F. R. Blattner, R. R. Chaudhuri, J. D. Glasner, T. Horiuchi, I. M. Keseler, T. Kosuge, et al. Escherichia coli K-12: a cooperatively developed annotation snapshot--2005 Nucleic Acids Res., January 5, 2006; 34(1): 1 - 9. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Robertson, M. Bilenky, K. Lin, A. He, W. Yuen, M. Dagpinar, R. Varhol, K. Teague, O. L. Griffith, X. Zhang, et al. cisRED: a database system for genome-scale computational discovery of regulatory elements Nucleic Acids Res., January 1, 2006; 34(suppl_1): D68 - D73. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. D. Schmid, R. Perier, V. Praz, and P. Bucher EPD in its twentieth year: towards complete promoter coverage of selected model organisms Nucleic Acids Res., January 1, 2006; 34(suppl_1): D82 - D85. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Jagannathan, E. Roulet, M. Delorenzi, and P. Bucher HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites Nucleic Acids Res., January 1, 2006; 34(suppl_1): D90 - D94. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Matys, O. V. Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I. Reuter, D. Chekmenev, M. Krull, K. Hornischer, et al. TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes Nucleic Acids Res., January 1, 2006; 34(suppl_1): D108 - D110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Mokrejs, V. Vopalensky, O. Kolenaty, T. Masek, Z. Feketova, P. Sekyrova, B. Skaloudova, V. Kriz, and M. Pospisek IRESite: the database of experimentally verified IRES structures (www.iresite.org) Nucleic Acids Res., January 1, 2006; 34(suppl_1): D125 - D130. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Dunin-Horkawicz, A. Czerwoniec, M. J. Gajda, M. Feder, H. Grosjean, and J. M. Bujnicki MODOMICS: a database of RNA modification pathways Nucleic Acids Res., January 1, 2006; 34(suppl_1): D145 - D149. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. H. Wu, R. Apweiler, A. Bairoch, D. A. Natale, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, et al. The Universal Protein Resource (UniProt): an expanding universe of protein information Nucleic Acids Res., January 1, 2006; 34(suppl_1): D187 - D191. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Letunic, R. R. Copley, B. Pils, S. Pinkert, J. Schultz, and P. Bork SMART 5: domains in the context of genomes and networks Nucleic Acids Res., January 1, 2006; 34(suppl_1): D257 - D260. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Pieper, N. Eswar, F. P. Davis, H. Braberg, M. S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B. M. Webb, D. Eramian, et al. MODBASE: a database of annotated comparative protein structure models and associated resources Nucleic Acids Res., January 1, 2006; 34(suppl_1): D291 - D295. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kouranov, L. Xie, J. de la Cruz, L. Chen, J. Westbrook, P. E. Bourne, and H. M. Berman The RCSB PDB information portal for structural genomics Nucleic Acids Res., January 1, 2006; 34(suppl_1): D302 - D305. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Castrignano, P. D. De Meo, D. Cozzetto, I. G. Talamo, and A. Tramontano The PMDB Protein Model Database Nucleic Acids Res., January 1, 2006; 34(suppl_1): D306 - D309. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. A. Eyre, F. Ducluzeau, T. P. Sneddon, S. Povey, E. A. Bruford, and M. J. Lush The HUGO Gene Nomenclature Database, 2006 updates Nucleic Acids Res., January 1, 2006; 34(suppl_1): D319 - D321. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Maltsev, E. Glass, D. Sulakhe, A. Rodriguez, M. H. Syed, T. Bompada, Y. Zhang, and M. D'Souza PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways Nucleic Acids Res., January 1, 2006; 34(suppl_1): D369 - D372. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Adams and J. F. Antoniw DPVweb: a comprehensive database of plant and fungal virus genes and genomes Nucleic Acids Res., January 1, 2006; 34(suppl_1): D382 - D385. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Mehrle, H. Rosenfelder, I. Schupp, C. del Val, D. Arlt, F. Hahne, S. Bechtel, J. Simpson, O. Hofmann, W. Hide, et al. The LIFEdb database in 2006 Nucleic Acids Res., January 1, 2006; 34(suppl_1): D415 - D418. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Guldener, G. Mannhaupt, M. Munsterkotter, D. Haase, M. Oesterheld, V. Stumpflen, H.-W. Mewes, and G. Adam FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum Nucleic Acids Res., January 1, 2006; 34(suppl_1): D456 - D458. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Sims, B. Bursteinas, Q. Gao, M. Zvelebil, and B. Baum FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets Nucleic Acids Res., January 1, 2006; 34(suppl_1): D479 - D483. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Ng, B. Bursteinas, Q. Gao, E. Mollison, and M. Zvelebil pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer Nucleic Acids Res., January 1, 2006; 34(suppl_1): D527 - D534. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Li, A. Coghlan, J. Ruan, L. J. Coin, J.-K. Heriche, L. Osmotherly, R. Li, T. Liu, Z. Zhang, L. Bolund, et al. TreeFam: a curated database of phylogenetic trees of animal gene families Nucleic Acids Res., January 1, 2006; 34(suppl_1): D572 - D580. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Lenffer, F. W. Nicholas, K. Castle, A. Rao, S. Gregory, M. Poidinger, M. D. Mailman, and S. Ranganathan |