Database resources of the National Center for Biotechnology Information

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Sayers, Eric W ^a   Barrett, Tanya ^a   Benson, Dennis A ^a   Bryant, Stephen H ^a   Canese, Kathi ^a   Chetvernin , Vyacheslav ^a   Church, Deanna M ^a   Dicuccio, Michael ^a   Edgar, Ron ^a   Federhen, Scott ^a   Feolo, Michael ^a   Geer, Lewis Y ^a   Helmberg, Wolfgang ^a   Kapustin, Yuri ^a   Landsman, David ^a   Lipman, David J ^a   Madden, Thomas L ^a   Maglott, Donna R ^a   Miller, Vadim ^a   Mizrachi, Ilene ^a   Ostell, James ^a   Pruitt, Kim D ^a   Schuler, Gregory D ^a   Sequeira, Edwin ^a   Sherry, Stephen T ^a   Shumway, Martin ^a   Sirotkin, Karl ^a   Souvorov, Alexandre ^a   Starchenko, Grigory ^a   Tatusova, Tatiana A ^a   Wagner, Lukas ^a   Yaschenko, Eugene ^a   Ye, Jian ^a   more..

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BIOASSAY; BIOINFORMATICS; BIOTECHNOLOGY; CHEMICAL STRUCTURE; COMPUTER PROGRAM; FACTUAL DATABASE; GENBANK; GENE CLUSTER; GENE EXPRESSION; GENE SEQUENCE; GENETIC DATABASE; GENOTYPE; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; INFORMATION RETRIEVAL; INHERITANCE; INTERNET; MEDLINE; MOLECULAR MODEL; NONHUMAN; NUCLEIC ACID DATABASE; ONLINE SYSTEM; ORTHOLOGY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEOMICS; RETROVIRUS; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; TAXONOMY; DATA ANALYSIS; DATA BASE; INFORMATION TECHNOLOGY; NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION; NATIONAL HEALTH ORGANIZATION; NUCLEOTIDE SEQUENCE;

DATABASES, GENETIC; GENE EXPRESSION; GENES; GENOMICS; GENOTYPE; NATIONAL LIBRARY OF MEDICINE (U.S.); PHENOTYPE; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; PUBMED; SEQUENCE HOMOLOGY; SYSTEMS INTEGRATION; UNITED STATES;

ANIMALIA; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 58149200954     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn741     Document Type: Article

References (49)

1. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Sayers,E.W. (2009) GenBank. Nucleic Acids Res., this issue.
2. Rozen,S. and Skalestsky,H.J. (2000) Primer3 on the WWW for general users and for biologist programmers. In Krawetz,S. and Misener,S. (eds), Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp. 365-386.
3. Johnson,M., Zaretskaya,I., Raytselis,Y., Merezhuk,Y., McGinnis,S. and Madden,T.L. (2008) NCBI BLAST: A better web interface. Nucleic Acids Res., 36, W5-9.
4. Schuler,G.D., Epstein,J.A., Ohkawa,H. and Kans,J.A. (1996) Entrez: molecular biology database and retrieval system. Meth. enzymol., 266, 141-162.
5. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
6. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
7. Ye,J., McGinnis,S. and Madden,T.L. (2006) BLAST: Improvements for better sequence analysis. Nucleic Acids Res., 34, W6-9.
8. Tatusova,T.A. and Madden,T.L. (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett., 174, 247-250.
9. Zhang,Z., Schwartz,S., Wagner,L. and Miller,W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 7, 203-214.
10. Sewell,W. (1964) Medical Subject Headings in Medlars. Bull. Med. Libr. Assoc., 52, 164-170.
11. Sequeira,E. (2003) PubMed Central - three years old and growing stronger. ARL, 228, 5-9.
12. Maglott,D., Ostell,J., Pruitt,K.D. and Tatusova,T. (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 35, D26-31.
13. Schuler,G.D. (1997) Pieces of the puzzle: Expressed sequence tags and the catalog of human genes. J. Mol. Med., 75, 694-698.
14. Ermolaeva,O., Rastogi,M., Pruitt,K.D., Schuler,G.D., Bittner,M.L., Chen,Y., Simon,R., Meltzer,P., Trent,J.M. and Boguski,M.S. (1998) Data management and analysis for gene expression arrays. Nat. genet., 20, 19-23.
15. Hamosh,A. (2009) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res., this issue.
16. Eppig,J.T., Blake,J.A., Bult,C.J., Kadin,J.A. and Richardson,J.E. (2007) The mouse genome database (MGD): New features facilitating a model system. Nucleic Acids Res., 35, D630-637.
17. Sprague,J., Bayraktaroglu,L., Clements,D., Conlin,T., Fashena,D., Frazer,K., Haendel,M., Howe,D.G., Mani,P., Ramachandran,S. et al. (2006) The Zebrafish Information Network: The zebrafish model organism database. Nucleic Acids Res., 34, D581-585.
18. Hong,E.L., Balakrishnan,R., Dong,Q., Christie,K.R., Park,J., Binkley,G., Costanzo,M.C., Dwight,S.S., Engel,S.R., Fisk,D.G. et al. (2008) Gene Ontology annotations at SGD: New data sources and annotation methods. Nucleic Acids Res., 36, D577-581.
19. Tatusov,R.L., Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V., Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N. et al. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
20. Crosby,M.A., Goodman,J.L., Strelets,V.B., Zhang,P. and Gelbart,W.M. (2007) FlyBase: Genomes by the dozen. Nucleic Acids Res., 35 D486-491.
21. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2009) NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., this issue.
22. Kapustin,Y., Souvorov,A., Tatusova,T. and Lipman,D. (2008) Splign: algorithms for computing spliced alignments with identification of paralogs. Biol. Direct, 3, 20.
23. Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
24. Tatusova,T.A., Karsch-Mizrachi,I. and Ostell,J.A. (1999) Complete genomes in WWW Entrez: Data representation and analysis. Bioinformatics, 15, 536-543.
25. Mitelman,F., Mertens,F. and Johansson,B. (1997) A breakpoint map of recurrent chromosomal rearrangements in human neoplasia. Nat. Genet. 15 (Spec No), 417-474.
26. Ghedin,E., Sengamalay,N.A., Shumway,M., Zaborsky,J., Feldblyum,T., Subbu,V., Spiro,D.J., Sitz,J., Koo,H., Bolotov,P. et al. (2005) Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature, 437, 1162-1166.
27. Klimke,W. (2009) Protein Clusters. Nucleic Acids Res., this issue.
28. Manolio,T.A., Rodriguez,L.L., Brooks,L., Abecasis,G., Ballinger,D., Daly,M., Donnelly,P., Faraone,S.V., Frazer,K., Gabriel,S. et al. (2007) New models of collaboration in genomewide association studies: the Genetic Association Information Network. Nat. Genet., 39 1045-1051.
29. Sherry,S.T., Ward,M.H., Kholodov,M., Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
30. Blumenfeld,O.O. and Patnaik,S.K. (2004) Allelic genes of blood group antigens: A source of human mutations and cSNPs documented in the Blood Group Antigen Gene Mutation Database. Human Mut., 23, 8-16.
31. Helmberg,W., Dunivin,R. and Feolo,M. (2004) The sequencing-based typing tool of dbMHC: Typing highly polymorphic gene sequences. Nucleic Acids Res., 32, W173-175.
32. Lenffer,J., Nicholas,F.W., Castle,K., Rao,A., Gregory,S., Poidinger,M., Mailman,M.D. and Ranganathan,S. (2006) OMIA (Online Mendelian Inheritance in Animals): An enhanced platform and integration into the Entrez search interface at NCBI. Nucleic Acids Res., 34, D599-601.
33. Barrett,T., Troup,D.B., Wilhite,S.E., Ledoux,P., Rudnev,D., Evangelista,C., Kim,I.F., Soboleva,A., Tomashevsky,M. and Edgar,R. (2009) NCBI GEO: Mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res., this issue.
34. Brazma,A., Hingamp,P., Quackenbush,J., Sherlock,G., Spellman,P., Stoeckert,C., Aach,J., Ansorge,W., Ball,C.A., Causton,H.C. et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet., 29, 365-371.
35. Whetzel,P.L., Parkinson,H., Causton,H.C., Fan,L., Fostel,J., Fragoso,G., Game,L., Heiskanen,M., Morrison,N., Rocca-Serra,P. et al. (2006) The MGED Ontology: A resource for semantics-based description of microarray experiments. Bioinformatics, 22, 866-873.
36. Geschwind,D. (2004) GENSAT: A genomic resource for neuroscience research. Lancet Neurol., 3, 82.
37. Gong,S., Zheng,C., Doughty,M.L., Losos,K., Didkovsky,N., Schambra,U.B., Nowak,N.J., Joyner,A., Leblanc,G., Hatten,M.E. et al. (2003) A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature, 425, 917-925.
38. Heintz,N. (2004) Gene expression nervous system atlas (GENSAT). Nat. Neurosci., 7, 483.
39. Wang,Y., Addess,K.J., Chen,J., Geer,L.Y., He,J., He,S., Lu,S., Madej,T., Marchler-Bauer,A., Thiessen,P.A. et al. (2007) MMDB: Annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res., 35, D298-300.
40. Berman,H., Henrick,K., Nakamura,H. and Markley,J.L. (2007) The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-303.
41. Marchler-Bauer,A., Anderson,J.B., Derbyshire,M.K., DeWeese-Scott,C., Gonzales,N.R., Gwadz,M., Hao,L., He,S., Hurwitz,D.I., Jackson,J.D. et al. (2009) CDD: A conserved domain database for interactive domain family analysis. Nucleic Acids Res., this issue.
42. Gibrat,J.F., Madej,T. and Bryant,S.H. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385.
43. Madej,T., Gibrat,J.F. and Bryant,S.H. (1995) Threading a database of protein cores. Proteins, 23, 356-369.
44. Wang,Y., Geer,L.Y., Chappey,C., Kans,J.A. and Bryant,S.H. (2000) Cn3D: sequence and structure views for Entrez. Trends Biochem. Sci., 25, 300-302.
45. Letunic,I., Copley,R.R., Pils,B., Pinkert,S., Schultz,J. and Bork,P. (2006) SMART 5: Domains in the context of genomes and networks. Nucleic Acids Res., 34, D257-260.
46. Finn,R.D., Mistry,J., Schuster-Bockler,B., Griffiths-Jones,S., Hollich,V., Lassmann,T., Moxon,S., Marshall,M., Khanna,A., Durbin,R. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res. 34, D247-251.
47. Geer,L.Y., Markey,S.P., Kowalak,J.A., Wagner,L., Xu,M., Maynard,D.M., Yang,X., Shi,W. and Bryant,S.H. (2004) Open mass spectrometry search algorithm. J. Proteome Res., 3, 958-964.
48. Fu,W. (2009) HIV Protein Interaction Database. Nucleic Acids Res., this issue.
49. Wang,Y. (2009) PubChem BioAssay. Nucleic Acids Res., this issue.