Database resources of the National Center for Biotechnology Information

Nucleic Acids Research

Volumn 35, Issue SUPPL. 1, 2007, Pages

  Wheeler, David L ^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   Geer, Lewis Y ^a   Kapustin, Yuri ^a   Khovayko, Oleg ^a   Landsman, David ^a   Lipman, David J ^a   Madden, Thomas L ^a   Maglott, Donna R ^a   Ostell, James ^a   Miller, Vadim ^a   Pruitt, Kim D ^a   Schuler, Gregory D ^a   Sequeira, Edwin ^a   Sherry, Steven T ^a   Sirotkin, Karl ^a   Souvorov, Alexandre ^a   Starchenko, Grigory ^a   Tatusov, Roman L ^a   Tatusova, Tatiana A ^a   Wagner, Lukas ^a   Yaschenko, Eugene ^a   more..

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID;

ARTICLE; BLAST LINK(BLINK); CANCER CHROMOSOMES; DATA ANALYSIS; DATA BASE; DBSNP; ELECTRONIC PCR; ENTREZ; ENTREZ GENE; ENTREZ GENOME; ENTREZ PROGRAMMING UTILITIES; FACTUAL DATABASE; GENBANK; GENOME PROJECT; HOMOLOGENE; INFORMATION RETRIEVAL; INFORMATION SYSTEM; INTERNET; MEDLINE; NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION; NCBI TAXONOMY BROWSER; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; ORGANIZATION; ORTFINDER; PRESSURE WAVE; PRIORITY JOURNAL; PROTEST; PUBMED CENTRAL; REFSEQ; SPIDEY; SPLIGN; UNIGENE;

ANIMALS; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; GENE EXPRESSION; GENOMICS; HUMANS; INTERNET; NATIONAL LIBRARY OF MEDICINE (U.S.); PHENOTYPE; PROTEOMICS; PUBMED; SEQUENCE ALIGNMENT; SOFTWARE; UNITED STATES;

ANIMALIA; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33846062023     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1031     Document Type: Article

References (36)

1. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Wheeler,D.L. (2006) GenBank. Nucleic Acids Res., 34, D16-D20.
2. Schuler,G.D., Epstein,J.A., Ohkawa,H. and Kans,J.A. (1996) Entrez: molecular biology database and retrieval system. Methods Enzymol., 266, 141-162.
3. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2005) NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.
4. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
5. Kouranov,A., Xie,L., de la Cruz,J., Chen,L., Westbrook,J., Bourne,P.E. and Berman,H.M. (2006) The RCSB PDB information portal for structural genomics. Nucleic Acids Res., 34, D302-D305.
6. Marchler-Bauer,A., Anderson,J.B., Cherukuri,P.F., DeWeese-Scott,C., Geer,L.Y., Gwadz,M., He,S., Hurwitz,D.I., Jackson,J.D., Ke,Z. et al. (2005) CDD: A Conserved Domain Database for protein classification. Nucleic Acids Res., 33, D192-D196.
7. Sewell,W. (1964) Medical Subject Headings in MEDLARS. Bull Med. Libr. Assoc., 52, 164-170.
8. Sequeira,E. (2003) PubMed central - three years old and growing stronger. ARL, 228, 5-9.
9. 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.
10. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
11. Ye,J., McGinnis,S. and Madden,T.L. (2006) BLAST: Improvements for better sequence analysis. Nucleic Acids Res., 34, W6-W9.
12. 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.
13. Schäffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L., Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
14. Zhang,Z., Schwartz,S., Wagner,L. and Miller,W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 7, 203-214.
15. Ma,B., Tromp,J. and Li,M. (2002) PatternHunter: Faster and more sensitive homology search. Bioinformatics, 18, 440-445.
16. Maglott,D., Ostell,J., Pruitt,K.D. and Tatusova,T. (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., this Issue.
17. Schuler,G.D. (1997) Pieces of the puzzle: Expressed sequence tags and the catalog of human genes. J. Mol. Med., 75, 694-698.
18. 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. Nature Genet., 20, 19-23.
19. Blake,J.A., Eppig,J.T., Bult,C.J., Kadin,J.A. and Richardson,J.E. (2006) The Mouse Genome Database (MGD): Updates and enhancements. Nucleic Acids Res., 34, D562-D567.
20. 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-D585.
21. Hirschman,J.E., Balakrishnan,R., Christie,K.R., Costanzo,M.C., Dwight,S.S., Engel,S.R., Fisk,D.G., Hong,E.L., Livstone,M.S., Nash,R. et al. (2006) Genome Snapshot: A new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res., 34, D442-D445.
22. 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.
23. 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.
24. 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.
25. Kapustin,Y., Souvorov,A. and Tatusova,T. (2004) Splign - a hybrid approach to spliced alignments. In Gramada,A. and Bourne,P. (eds), Eighth Annual International Conference on RECOMB 2004 - Currents in Computational Molecular Biol., p. 741.
26. 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.
27. Tatusova,T.A., Karsch-Mizrachi,I. and Ostell,J.A. (1999) Complete genomes in WWW Entrez: Data representation and analysis. Bioinformatics, 15, 536-543.
28. Mitelman,F., Mertens,F. and Johansson,B. (1997) A breakpoint map of recurrent chromosomal rearrangements in human neoplasia. Nature Genet., 15, 417-474.
29. 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.
30. Barrett,T., Troup,D.B., Wilhite,S.E., Ledoux,P., Rudnev,D., Evangelista,C., Kim,I.F., Soboleva,A., Tomashevsky,M. and Edgar,R. (2007) NCBI GEO: Mining tens of millions of expression profiles - database and tools update. Nucleic Acids Res., this Issue (Database Issue).
31. McKusick,V.A. (1998) Mendelian Inheritance in Man. Catalogs of Human Genes and Genetic Disorders. The Johns Hopkins University Press, Baltimore.
32. Hamosh,A., Scott,A.F., Amberger,J.S., Bocchini,C.A. and McKusick,V.A. (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res., 33, D514-D517.
33. Chen,J., Anderson,J.B., DeWeese-Scott,C., Fedorova,N.D., Geer,L.Y., He,S., Hurwitz,D.I., Jackson,J.D., Jacobs,A.R., Lanczycki,C.J. et al. (2003) MMDB: Entrez's 3D-structure database. Nucleic Acids Res., 31, 474-477.
34. 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-D260.
35. 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-D251.
36. 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.