Literature DB >> 12519941

Database resources of the National Center for Biotechnology.

David L Wheeler1, Deanna M Church, Scott Federhen, Alex E Lash, Thomas L Madden, Joan U Pontius, Gregory D Schuler, Lynn M Schriml, Edwin Sequeira, Tatiana A Tatusova, Lukas Wagner.   

Abstract

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, 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 data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Entities:  

Mesh:

Year:  2003        PMID: 12519941      PMCID: PMC165480          DOI: 10.1093/nar/gkg033

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


  24 in total

1.  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

2.  Complete genomes in WWW Entrez: data representation and analysis.

Authors:  T A Tatusova; I Karsch-Mizrachi; J A Ostell
Journal:  Bioinformatics       Date:  1999 Jul-Aug       Impact factor: 6.937

Review 3.  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

4.  GenBank.

Authors:  Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; Barbara A Rapp; David L Wheeler
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

Authors:  Ron Edgar; Michael Domrachev; Alex E Lash
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

6.  PatternHunter: faster and more sensitive homology search.

Authors:  Bin Ma; John Tromp; Ming Li
Journal:  Bioinformatics       Date:  2002-03       Impact factor: 6.937

7.  MMDB: Entrez's 3D-structure database.

Authors:  Jie Chen; John B Anderson; Carol DeWeese-Scott; Natalie D Fedorova; Lewis Y Geer; Siqian He; David I Hurwitz; John D Jackson; Aviva R Jacobs; Christopher J Lanczycki; Cynthia A Liebert; Chunlei Liu; Thomas Madej; Aron Marchler-Bauer; Gabriele H Marchler; Raja Mazumder; Anastasia N Nikolskaya; Bachoti S Rao; Anna R Panchenko; Benjamin A Shoemaker; Vahan Simonyan; James S Song; Paul A Thiessen; Sona Vasudevan; Yanli Wang; Roxanne A Yamashita; Jodie J Yin; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

8.  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

9.  Recent improvements to the SMART domain-based sequence annotation resource.

Authors:  Ivica Letunic; Leo Goodstadt; Nicholas J Dickens; Tobias Doerks; Joerg Schultz; Richard Mott; Francesca Ciccarelli; Richard R Copley; Chris P Ponting; Peer Bork
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

10.  The Pfam protein families database.

Authors:  Alex Bateman; Ewan Birney; Lorenzo Cerruti; Richard Durbin; Laurence Etwiller; Sean R Eddy; Sam Griffiths-Jones; Kevin L Howe; Mhairi Marshall; Erik L L Sonnhammer
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

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  363 in total

1.  Genew: the Human Gene Nomenclature Database, 2004 updates.

Authors:  Hester M Wain; Michael J Lush; Fabrice Ducluzeau; Varsha K Khodiyar; Sue Povey
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries.

Authors:  Hirohide Uenishi; Tomoko Eguchi; Kohei Suzuki; Tetsuya Sawazaki; Daisuke Toki; Hiroki Shinkai; Naohiko Okumura; Noriyuki Hamasima; Takashi Awata
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  The Mouse SAGE Site: database of public mouse SAGE libraries.

Authors:  Petr Divina; Jirí Forejt
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  GermOnline, a cross-species community knowledgebase on germ cell differentiation.

Authors:  C Wiederkehr; R Basavaraj; C Sarrauste de Menthière; L Hermida; R Koch; U Schlecht; A Amon; S Brachat; M Breitenbach; P Briza; S Caburet; M Cherry; R Davis; A Deutschbauer; H G Dickinson; T Dumitrescu; M Fellous; A Goldman; J A Grootegoed; R Hawley; R Ishii; B Jégou; R J Kaufman; F Klein; N Lamb; B Maro; K Nasmyth; A Nicolas; T Orr-Weaver; P Philippsen; C Pineau; K P Rabitsch; V Reinke; H Roest; W Saunders; M Schröder; T Schedl; M Siep; A Villeneuve; D J Wolgemuth; M Yamamoto; D Zickler; R E Esposito; M Primig
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  The mouse Gene Expression Database (GXD): updates and enhancements.

Authors:  David P Hill; Dale A Begley; Jacqueline H Finger; Terry F Hayamizu; Ingeborg J McCright; Constance M Smith; Jon S Beal; Lori E Corbani; Judith A Blake; Janan T Eppig; James A Kadin; Joel E Richardson; Martin Ringwald
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  MaizeGDB, the community database for maize genetics and genomics.

Authors:  Carolyn J Lawrence; Qunfeng Dong; Mary L Polacco; Trent E Seigfried; Volker Brendel
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

7.  Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

Authors:  Karen R Christie; Shuai Weng; Rama Balakrishnan; Maria C Costanzo; Kara Dolinski; Selina S Dwight; Stacia R Engel; Becket Feierbach; Dianna G Fisk; Jodi E Hirschman; Eurie L Hong; Laurie Issel-Tarver; Robert Nash; Anand Sethuraman; Barry Starr; Chandra L Theesfeld; Rey Andrada; Gail Binkley; Qing Dong; Christopher Lane; Mark Schroeder; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

8.  SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes.

Authors:  Bernice R Packer; Meredith Yeager; Brian Staats; Robert Welch; Andrew Crenshaw; Maureen Kiley; Andrew Eckert; Michael Beerman; Edward Miller; Andrew Bergen; Nathaniel Rothman; Robert Strausberg; Stephen J Chanock
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

9.  Periplasmic cleavage and modification of the 1-phosphate group of Helicobacter pylori lipid A.

Authors:  An X Tran; Mark J Karbarz; Xiaoyuan Wang; Christian R H Raetz; Sara C McGrath; Robert J Cotter; M Stephen Trent
Journal:  J Biol Chem       Date:  2004-10-15       Impact factor: 5.157

10.  Acetylornithine transcarbamylase: a novel enzyme in arginine biosynthesis.

Authors:  Hiroki Morizono; Juan Cabrera-Luque; Dashuang Shi; Rene Gallegos; Saori Yamaguchi; Xiaolin Yu; Norma M Allewell; Michael H Malamy; Mendel Tuchman
Journal:  J Bacteriol       Date:  2006-04       Impact factor: 3.490

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