Biomedical & Genomic Information Resources from NCBI

Dec. 20, 2013 - The National Center for Biotechnology Information (NCBI), part of the National Library of Medicine, "advances science and health by providing access to biomedical and genomic information."  Most people have heard of PubMed, NCBI's world famous biomedical citation and abstract database, but NCBI is responsible for over 150 other databases, resources, and tools that are vital to research in areas ranging from basic science to personalized medicine.  And these resources are all freely available to researchers who need them (some resources do require special account creation due to sensitive information).

The north display case outside of the Todd Wehr Library is currently highlighting the NCBI and its resources, and includes some Cn3D images from MCW research.

Here are just a few of NCBI's featured databases and resources :Todd Wehr Library North Display Case: NCBI Resources

  • Basic Local Alignment Search Tool (BLAST): finds regions of local similarity between 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 help identify members of gene families.
  • Cn3D ("see in 3D"): a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez Structure database. Cn3D is provided for Windows and Macintosh, and can be compiled on Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.
  • dbGaP: the database of Genotypes and Phenotypes, developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype.
  • dbSNP: database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants.
  • Gene: integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
  • OMIM: a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. Its official home is omim.org
  • Protein: a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from Swiss-Prot, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.
  • RefSeq: a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

The MCW Libraries are equipped to provide education and support on NCBI's resources, and can help answer your questions using these tools.  We also have a librarian on staff who has been trained in-person at NCBI in their use.  Set up a one-on-one training session using our training request form, or contact us at 414.955.8302 or asklib@mcw.edu for more information!

 

 

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