Literature DB >> 11125038

Database resources of the National Center for Biotechnology Information.

D L Wheeler1, D M Church, A E Lash, D D Leipe, T L Madden, J U Pontius, G D Schuler, L M Schriml, T A Tatusova, L Wagner, B A Rapp.   

Abstract

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap'99, Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri-tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). 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.

Entities:  

Mesh:

Year:  2001        PMID: 11125038      PMCID: PMC29800          DOI: 10.1093/nar/29.1.11

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  22 in total

1.  MMDB: 3D structure data in Entrez.

Authors:  Y Wang; K J Addess; L Geer; T Madej; A Marchler-Bauer; D Zimmerman; S H Bryant
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  SMART: a web-based tool for the study of genetically mobile domains.

Authors:  J Schultz; R R Copley; T Doerks; C P Ponting; P Bork
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  dbSNP: the NCBI database of genetic variation.

Authors:  S T Sherry; M H Ward; M Kholodov; J Baker; L Phan; E M Smigielski; K Sirotkin
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

4.  RefSeq and LocusLink: NCBI gene-centered resources.

Authors:  K D Pruitt; D R Maglott
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

5.  CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.

Authors:  E V Kriventseva; W Fleischmann; E M Zdobnov; R Apweiler
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

6.  Cn3D: sequence and structure views for Entrez.

Authors:  Y Wang; L Y Geer; C Chappey; J A Kans; S H Bryant
Journal:  Trends Biochem Sci       Date:  2000-06       Impact factor: 13.807

7.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

Review 8.  A gene map of the human genome.

Authors:  G D Schuler; M S Boguski; E A Stewart; L D Stein; G Gyapay; K Rice; R E White; P Rodriguez-Tomé; A Aggarwal; E Bajorek; S Bentolila; B B Birren; A Butler; A B Castle; N Chiannilkulchai; A Chu; C Clee; S Cowles; P J Day; T Dibling; N Drouot; I Dunham; S Duprat; C East; C Edwards; J B Fan; N Fang; C Fizames; C Garrett; L Green; D Hadley; M Harris; P Harrison; S Brady; A Hicks; E Holloway; L Hui; S Hussain; C Louis-Dit-Sully; J Ma; A MacGilvery; C Mader; A Maratukulam; T C Matise; K B McKusick; J Morissette; A Mungall; D Muselet; H C Nusbaum; D C Page; A Peck; S Perkins; M Piercy; F Qin; J Quackenbush; S Ranby; T Reif; S Rozen; C Sanders; X She; J Silva; D K Slonim; C Soderlund; W L Sun; P Tabar; T Thangarajah; N Vega-Czarny; D Vollrath; S Voyticky; T Wilmer; X Wu; M D Adams; C Auffray; N A Walter; R Brandon; A Dehejia; P N Goodfellow; R Houlgatte; J R Hudson; S E Ide; K R Iorio; W Y Lee; N Seki; T Nagase; K Ishikawa; N Nomura; C Phillips; M H Polymeropoulos; M Sandusky; K Schmitt; R Berry; K Swanson; R Torres; J C Venter; J M Sikela; J S Beckmann; J Weissenbach; R M Myers; D R Cox; M R James; D Bentley; P Deloukas; E S Lander; T J Hudson
Journal:  Science       Date:  1996-10-25       Impact factor: 47.728

9.  Entrez: molecular biology database and retrieval system.

Authors:  G D Schuler; J A Epstein; H Ohkawa; J A Kans
Journal:  Methods Enzymol       Date:  1996       Impact factor: 1.600

10.  The COG database: new developments in phylogenetic classification of proteins from complete genomes.

Authors:  R L Tatusov; D A Natale; I V Garkavtsev; T A Tatusova; U T Shankavaram; B S Rao; B Kiryutin; M Y Galperin; N D Fedorova; E V Koonin
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

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  103 in total

Review 1.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Authors:  A A Schäffer; L Aravind; T L Madden; S Shavirin; J L Spouge; Y I Wolf; E V Koonin; S F Altschul
Journal:  Nucleic Acids Res       Date:  2001-07-15       Impact factor: 16.971

2.  GeneLynx: a gene-centric portal to the human genome.

Authors:  B Lenhard; W S Hayes; W W Wasserman
Journal:  Genome Res       Date:  2001-12       Impact factor: 9.043

3.  Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences.

Authors:  Cecilia Lanave; Flavio Licciulli; Mariateresa De Robertis; Alessandra Marolla; Marcella Attimonelli
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

4.  CDD: a database of conserved domain alignments with links to domain three-dimensional structure.

Authors:  Aron Marchler-Bauer; Anna R Panchenko; Benjamin A Shoemaker; Paul A Thiessen; Lewis Y Geer; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  Wanda: a database of duplicated fish genes.

Authors:  Yves Van de Peer; John S Taylor; Jayabalan Joseph; Axel Meyer
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  FUGOID: functional genomics of organellar introns database.

Authors:  Fei Li; David L Herrin
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

7.  JSNP: a database of common gene variations in the Japanese population.

Authors:  Mika Hirakawa; Toshihiro Tanaka; Yoichi Hashimoto; Masako Kuroda; Toshihisa Takagi; Yusuke Nakamura
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

8.  AngioDB: database of angiogenesis and angiogenesis-related molecules.

Authors:  Tae-Kwon Sohn; Eun-Joung Moon; Seok-Ki Lee; Hwan-Gue Cho; Kyu-Won Kim
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

9.  S/MARt DB: a database on scaffold/matrix attached regions.

Authors:  Ines Liebich; Jürgen Bode; Matthias Frisch; Edgar Wingender
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

10.  CSDBase: an interactive database for cold shock domain-containing proteins and the bacterial cold shock response.

Authors:  Michael H W Weber; Ingo Fricke; Niclas Doll; Mohamed A Marahiel
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

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