NCBI Resources
NCBI Resources provide access to integrated biological databases, computational tools, and programmatic services—including GenBank and PubMed—for sequence, structural, variation, and literature analysis in genomics, proteomics, metabolomics, and medical research.
Key Features:
- Entrez System: The Entrez search and retrieval system enables unified querying across 34–39 databases and exposes E-utilities as a programming interface for automated queries and data retrieval.
- BLAST Tools: Custom implementations of the Basic Local Alignment Search Tool (BLAST) perform sequence similarity searches for nucleotide and protein sequences, optimized for specialized datasets.
- GenBank® Database: GenBank is a continuously updated repository of publicly available nucleic acid sequences and associated metadata.
- PubMed® and Related Resources: PubMed provides citations and abstracts for life science journals and is complemented by PubMed Central (PMC), Bookshelf, and PubReader for full-text and literature access.
- Genomic and Genetic Databases: Collections including BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene Expression Omnibus (GEO), Genome, HomoloGene, Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, Taxonomy Browser, Trace Archive, and UniGene support gene expression, variation, assembly, and comparative genomics data.
- Protein and Chemical Databases: Conserved Domain Database (CDD), Molecular Modeling Database (MMDB), Protein Clusters, Biosystems, and the PubChem suite provide data on protein domains, structures, clustering, pathway annotation, and small molecules.
- Medical and Health-Related Tools: ClinVar, dbGaP, dbMHC, Genetic Testing Registry, HIV-1/Human Protein Interaction Database, MedGen, and the Pathogen Detection Project provide clinical variant curation, genotype–phenotype data, HLA/MHC resources, genetic test metadata, host–pathogen interaction data, medical genetics information, and pathogen surveillance.
- New and Updated Resources: Recent additions and updates include iCn3D for molecular visualization, MutaBind for mutation analysis, the Antimicrobial Resistance Gene Reference Database, and updates to Genome Data Viewer, Assembly, BLAST databases, and PubChem.
Scientific Applications:
- Sequence alignment and homology searches: Perform nucleotide and protein sequence alignment and homology searches using BLAST-based resources.
- Gene expression analysis: Analyze and compare gene expression datasets using GEO and related expression databases.
- Protein structure modeling: Support protein structure inspection and conserved-domain analysis using MMDB and CDD.
- Genetic variation studies: Investigate population and clinical variants using dbSNP, dbVar, ClinVar, and dbGaP.
- Pathogen detection: Detect and surveil pathogens using the Pathogen Detection Project and sequence repositories.
- Exploration of molecular interactions: Study molecular and host–pathogen interactions using Protein Clusters, Biosystems, and the HIV-1/Human Protein Interaction Database.
- Hypothesis generation and data mining: Enable large-scale hypothesis generation and data mining across integrated databases via Entrez and programmatic access.
- Validation of experimental results: Provide reference sequences and curated datasets (RefSeq, GenBank, SRA) for validation and reproducibility of experimental findings.
Methodology:
Sequence similarity searching using BLAST (Basic Local Alignment Search Tool), programmatic data retrieval via Entrez E-utilities, molecular visualization with iCn3D, and mutation analysis with MutaBind.
Topics
Collections
Details
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 3/30/2017
- Last Updated:
- 6/27/2022
Operations
Publications
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2009;38(suppl_1):D5-D16. doi:10.1093/nar/gkp967. PMID:19910364. PMCID:PMC2808881.
Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, Bourexis D, Brister JR, Bryant SH, Canese K, Cavanaugh M, Charowhas C, Clark K, Dondoshansky I, Feolo M, Fitzpatrick L, Funk K, Geer LY, Gorelenkov V, Graeff A, Hlavina W, Holmes B, Johnson M, Kattman B, Khotomlianski V, Kimchi A, Kimelman M, Kimura M, Kitts P, Klimke W, Kotliarov A, Krasnov S, Kuznetsov A, Landrum MJ, Landsman D, Lathrop S, Lee JM, Leubsdorf C, Lu Z, Madden TL, Marchler-Bauer A, Malheiro A, Meric P, Karsch-Mizrachi I, Mnev A, Murphy T, Orris R, Ostell J, O'Sullivan C, Palanigobu V, Panchenko AR, Phan L, Pierov B, Pruitt KD, Rodarmer K, Sayers EW, Schneider V, Schoch CL, Schuler GD, Sherry ST, Siyan K, Soboleva A, Soussov V, Starchenko G, Tatusova TA, Thibaud-Nissen F, Todorov K, Trawick BW, Vakatov D, Ward M, Yaschenko E, Zasypkin A, Zbicz K. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2017;46(D1):D8-D13. doi:10.1093/nar/gkx1095. PMID:29140470. PMCID:PMC5753372.
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2010;39(Database):D38-D51. doi:10.1093/nar/gkq1172. PMID:21097890. PMCID:PMC3013733.
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Krasnov S, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Karsch-Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2011;40(D1):D13-D25. doi:10.1093/nar/gkr1184. PMID:22140104. PMCID:PMC3245031.
Wheeler DL. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2004;33(Database issue):D39-D45. doi:10.1093/nar/gki062. PMID:15608222. PMCID:PMC540016.
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2007;35(Database):D5-D12. doi:10.1093/nar/gkl1031. PMID:17170002. PMCID:PMC1781113.
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2007;36(Database):D13-D21. doi:10.1093/nar/gkm1000. PMID:18045790. PMCID:PMC2238880.
Unknown Authors. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2014;43(D1):D6-D17. doi:10.1093/nar/gku1130. PMID:25398906. PMCID:PMC4383943.
Unknown Authors. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2015;44(D1):D7-D19. doi:10.1093/nar/gkv1290. PMID:26615191. PMCID:PMC4702911.
Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, Connor R, Funk K, Kelly C, Kim S, Madej T, Marchler-Bauer A, Lanczycki C, Lathrop S, Lu Z, Thibaud-Nissen F, Murphy T, Phan L, Skripchenko Y, Tse T, Wang J, Williams R, Trawick BW, Pruitt KD, Sherry ST. Database resources of the national center for biotechnology information. Nucleic Acids Research. 2021;50(D1):D20-D26. doi:10.1093/nar/gkab1112. PMID:34850941. PMCID:PMC8728269.
Sayers EW, Beck J, Bolton EE, Bourexis D, Brister JR, Canese K, Comeau DC, Funk K, Kim S, Klimke W, Marchler-Bauer A, Landrum M, Lathrop S, Lu Z, Madden TL, O’Leary N, Phan L, Rangwala SH, Schneider VA, Skripchenko Y, Wang J, Ye J, Trawick BW, Pruitt KD, Sherry ST. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2020;49(D1):D10-D17. doi:10.1093/nar/gkaa892. PMID:33095870. PMCID:PMC7778943.
Sayers EW, Beck J, Brister JR, Bolton EE, Canese K, Comeau DC, Funk K, Ketter A, Kim S, Kimchi A, Kitts PA, Kuznetsov A, Lathrop S, Lu Z, McGarvey K, Madden TL, Murphy TD, O’Leary N, Phan L, Schneider VA, Thibaud-Nissen F, Trawick BW, Pruitt KD, Ostell J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2019;48(D1):D9-D16. doi:10.1093/nar/gkz899. PMID:31602479. PMCID:PMC6943063.
Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K, Clark K, Connor R, Fiorini N, Funk K, Hefferon T, Holmes JB, Kim S, Kimchi A, Kitts PA, Lathrop S, Lu Z, Madden TL, Marchler-Bauer A, Phan L, Schneider VA, Schoch CL, Pruitt KD, Ostell J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2018;47(D1):D23-D28. doi:10.1093/nar/gky1069. PMID:30395293. PMCID:PMC6323993.
Unknown Authors. Database Resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2016;45(D1):D12-D17. doi:10.1093/nar/gkw1071. PMID:27899561. PMCID:PMC5210554.