Hardin Library
Submission to NCBI
Have General Library Questions?
Getting Started
The following are some of the more popular resources from the National Center for Biotechnology Information (NCBI).
When using BLAST, click the Help button to access the BLAST tutorials.
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Access all of the NCBI DatabasesThe National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
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Basic Local Alignment Search Tool (BLAST)Finds regions of local similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families.
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GeneA searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific data. Information includes nomenclature, chromosomal localization, gene products and their attributes (e.g., protein interactions), associated markers, phenotypes, interactions, and links to citations, sequences, variation details, maps, expression reports, homologs, protein domain content, and external databases.
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NucleotideA collection of nucleotide sequences from several sources, including GenBank, RefSeq, the Third Party Annotation (TPA) database, and PDB. Searching the Nucleotide Database will yield available results from each of its component databases.
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ProteinThe Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.
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Structure (Molecular Modeling Database)The Molecular Modeling Database (MMDB) contains 3D macromolecular structures, including proteins and polynucleotides. MMDB contains over 40,000 structures and is linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxon.
Nucleotide Sequences
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Expressed Sequence TagsIn the process of being merged with the Nucleotide DB, see below.
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Genome Survey SequencesAs of December 1, 2018, all records from the databases for Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS) will reside in NCBI’s Nucleotide database.
Protein and Protein Structure
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Conserved Domain DatabaseThe Conserved Domain Database (CDD) contains protein domain models imported from outside sources, such as Pfam and SMART, and curated at NCBI. CDD contains over 12,000 such models and is linked to other NCBI databases, including protein sequences, bibliog
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Protein Data BankThe PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.
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Protein ClustersThis collection of related protein sequences (clusters) consists of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.
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Human ProteinpediaHuman Proteinpedia is a community portal for sharing and integration of human protein data. It allows research laboratories to contribute and maintain protein annotations.
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ProDomProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database
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Protein Structure InitiativeThe long-range goal of the Protein Structure Initiative (PSI) is to make the three-dimensional atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences.
Genomes and Maps
NCBI Tools
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Map Vieweris a genome viewing browser from the NCBI. Map Viewer organizes and displays dozens of species genomes, and provides additional context with appropriate annotations for the genomic sequences.
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BLAST allBLAST finds regions of similarity between biological sequences
Biomedical Sciences Librarian
Mirko von Elstermann
Contact:
Hardin Library for the Health Sciences
Office: 2nd floor, 207A
600 Newton Road
Iowa City, Iowa 52242-1098
Phone 319-335-9153
Fax 319-353-3752
Website
Office: 2nd floor, 207A
600 Newton Road
Iowa City, Iowa 52242-1098
Phone 319-335-9153
Fax 319-353-3752
About Mirko
Education:
PhD, Physiology (cancer glycobiology)
MSc, Biology (bacterial metabolomics)
MA, Philosophy (systems theory)
MAS, Library & Information Sciences (biomedical library resources & services)
Work:
As an editor—Nature Publishing Group; Wiley-VCH; IGHPE; freelancing
As a librarian—University of Basel (CH); University of Veterinary Medicine (Hanover, DE), Weill Cornell Medicine-Qatar (Doha) Started at Hardin May 31st, 2017.