Literature DB >> 11752242

Database resources of the National Center for Biotechnology Information: 2002 update.

David L Wheeler1, Deanna M Church, Alex E Lash, Detlef D Leipe, Thomas L Madden, Joan U Pontius, Gregory D Schuler, Lynn M Schriml, Tatiana A Tatusova, Lukas Wagner, Barbara 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, Human inverted exclamation markVMouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, 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) 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.

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Year:  2002        PMID: 11752242      PMCID: PMC99094          DOI: 10.1093/nar/30.1.13

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


  21 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
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.  The Pfam protein families database.

Authors:  A Bateman; E Birney; R Durbin; S R Eddy; K L Howe; E L Sonnhammer
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

4.  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

5.  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

6.  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

7.  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

8.  A greedy algorithm for aligning DNA sequences.

Authors:  Z Zhang; S Schwartz; L Wagner; W Miller
Journal:  J Comput Biol       Date:  2000 Feb-Apr       Impact factor: 1.479

Review 9.  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

10.  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

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  73 in total

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

Authors:  Yanli Wang; John B Anderson; Jie Chen; Lewis Y Geer; Siqian He; David I Hurwitz; Cynthia A Liebert; Thomas Madej; Gabriele H Marchler; Aron Marchler-Bauer; Anna R Panchenko; Benjamin A Shoemaker; James S Song; Paul A Thiessen; Roxanne A Yamashita; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  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

3.  Cyclic coordinate descent: A robotics algorithm for protein loop closure.

Authors:  Adrian A Canutescu; Roland L Dunbrack
Journal:  Protein Sci       Date:  2003-05       Impact factor: 6.725

4.  GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.

Authors:  J Lin; J Qian; D Greenbaum; P Bertone; R Das; N Echols; A Senes; B Stenger; M Gerstein
Journal:  Nucleic Acids Res       Date:  2002-10-15       Impact factor: 16.971

5.  NLP-based information extraction for managing the molecular biology literature.

Authors:  Bisharah Libbus; Thomas C Rindflesch
Journal:  Proc AMIA Symp       Date:  2002

6.  Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population.

Authors:  Yun Freudenberg-Hua; Jan Freudenberg; Nadine Kluck; Sven Cichon; Peter Propping; Markus M Nöthen
Journal:  Genome Res       Date:  2003-10       Impact factor: 9.043

7.  Gene indexing: characterization and analysis of NLM's GeneRIFs.

Authors:  Joyce A Mitchell; Alan R Aronson; James G Mork; Lillian C Folk; Susanne M Humphrey; Janice M Ward
Journal:  AMIA Annu Symp Proc       Date:  2003

8.  A prototype system for retrieval of gene functional information.

Authors:  Lillian C Folk; Timothy B Patrick; Joyce S Pattison; Russell D Wolfinger; Joyce A Mitchell
Journal:  AMIA Annu Symp Proc       Date:  2003

9.  NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0.

Authors:  Wing Lok Abe Kurtz Chiu; Chun Ngai Sze; Nap Tak Ma; Lai Fan Chiu; Chung Wai Leung; Steve Chik Fun Au-Yeung
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

10.  TMPDB: a database of experimentally-characterized transmembrane topologies.

Authors:  Masami Ikeda; Masafumi Arai; Toshikatsu Okuno; Toshio Shimizu
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

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