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NCBI Bioinformatics Resources for Biosciences Researchers


What is NCBI?

NCBI is the National Center for Biotechnology Information.  The Center was founded in 1988 as a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH).  The NCBI website contains several free computerized information-processing methods of biological information.
 
NCBI not only conducts research on biomedical problems at the molecular level using mathematical and computational methods, but also provides numerous free databases and molecular search tools, with extensive support documentation for these resources.
 

Using This Guide

This guide is the same as the handout used in the Introduction to NCBI's Bioinformatics Resources class offered by Galter Library.   The class is only offered twice a year, but you can always schedule a session by request, or use this online guide to learn at your own pace.

If you would like to follow the steps and examples described in this guide, it is recommended that you open the NCBI website in another browser window and re-size the browser windows so both the guide and the NCBI pages can be viewed simultaneously.

Currently there is one video tutorial contained in this guide, located in the MapViewer section.  More videos are being developed and will be added to this guide as they are created. 

 

Why Use NCBI?

  • The Entrez search of NCBI allows a search across all databases:  Genome, Gene, Protein, Nucleotide, even PubMed
  • NCBI gives you real-time results for all searches
  • NCBI’s multi-database management allows you to go from one database to another without having to re-enter your search terms
 

Accessing NCBI’s Cross-Database Search Page

Go to http://www.ncbi.nlm.nih.gov/

 

NCBI_home_page

 

Navigation Hints

There are shortcuts and menus on all NCBI database pages:

  • Top-of-page menu bar shortcuts will take you to other major NCBI tools
  • Right-side pull-down menus for each entry will take you to related records
  • To get back to the NCBI home page at any time, just click the NCBI logo in the upper left of any screen 

Start with a General Search

Search terms can be entered just as in PubMed: 

  • You can use Boolean terms (AND, OR)
  • You can supply qualifiers in square brackets [au] = author, [organism], etc.

Try a search for “tubby” (a gene for obesity in mice with homologues in humans, rats, and other species) and “homo sapiens” as organism:

 

Entrez_search_results
 

MapViewer (with Video Tutorial)

 

MapViewer

 

On this screen

  • Use Maps & Options button to view the genomic maps of other species in this region for interspecies homology or to add specific types of maps to view (CpG islands, etc.)
  • View contigs, coding sequences
  • View neighboring genes
  • Zoom in or zoom out
  • BLAST the human genome using the direct link to genomic BLAST
  • Link to other databases, such as OMIM, through the links in the pinkish menu bar

 

 

  • Click on the SNP link in the pinkish label box
 

Entrez SNP

 

 

Entrez SNP record

 

 On this screen

  • View location and type of SNPs on a gene model, and link to each record in the Entrez SNP database
  • Link to HapMap data for variation in your gene or to Entrez Gene record
  • Link to records for genome contig, mRNA and protein records for your gene
  • View types of validation models for SNPs
  • Click on the mRNA link in the gene model box (NM_177972)
 

GenBank: NCBI’s Genetic Information Repository and Entrez Nucleotide Database

 

Entrez_nucleotide_record
 

 

On this screen

  • Display allows you to view records as FASTA, GenBank or other styles
  • Mark a record by clicking the checkbox beside an entry
  • Set limits for a more defined search
  • View the full record for any entry by clicking its Name/title

None of the records on this first page appear to be tubby itself, but Entrez helpfully suggests links in the Entrez Gene database that may be related to your search, so click on the link to the Entrez Gene record for “TUB” in the Gene results box at the top of the page.

 

Entrez Gene

 

Entrez_gene_record

 

On this screen

  • Link to related records in other NCBI databases through menu on right
  • Jump to Map Viewer or Sequence Viewer
  • Read GeneRIFs (references from the literature supporting the genes function)
  • View transcript regions and protein products
  • See where the gene lies on the chromosome and its nearest neighbors
  • View information from other databases such as Gene Ontology
  • For more detail on the gene, its location on the chromosome and homologous genes in other species, go to Map Viewer
  • Click "See TUB in Map Viewer"
 

Further Help

For assistance in using any of the NCBI tools and databases, email or call (312-503-8689) Pamela Shaw, Biosciences & Bioinformatics Librarian.

 

Entrez Nucleotide

 

Entrez Nucleotide record

 

On this screen

  • Links pull-down menu to right allows you to link to related records for this entry in other NCBI databases
  • Click Protein

 

 

Entrez Protein

 

Entrez protein entry page

 

 

Entrez Protein record

 

On this screen

  • Set Limits, change the Display
  • Through the drop-down Links menu:
    • Do a quick BLink (BLAST Link) to get an automatic BLAST of similar proteins
    • Check the protein for Conserved Domains
  • Check the sequence Revision History (More Formats drop-down menu)
  • Click BLink (from the pull-down Links menu)
 

Viewing Related Sequences and Structures

Performing a BLAST through the BLAST interface requires you to enter the sequence as FASTA format.  Clicking the BLink link from any protein record will take you to a page of pre-run BLAST sequence similarities.

 

BLink

 

 

 

Other Useful Databases and Tools @ NCBI

NCBI Educational Resources

The NCBI Education Page includes links to all sorts of NCBI tutorials and materials including:

  • NCBI Handbook
  • BLAST Tutorial
  • BLAST Guide
  • Cn3D Structure tutorial
  • NCBI’s Science Primer
 

The MMDB and Viewing Structures with Cn3D

From your Protein view page, check the links on the right for a Structure or Related Structure link.   If there are no solved structures or related structures for your protein, you won't see any structure links.

Alternatively, you can go back to the NCBI home page at http://www.ncbi.nlm.nih.gov/ and search for your protein structure by setting the pull-down menu to Structure and typing your query protein in the search box (eg., tubby).  This will give you a list of possible crystal structures for your protein.  Select one by clicking on the Accession Number.  This will take you to the MMDB (Molecular Modeling Database) structure page.

 

MMDB pages

 

On the Structure Summary screen

  • View the crystal structure of the protein
  • Run a structure similarity search (VAST) which finds other proteins with similar 3D structures (different from BLAST, which finds sequence similarities) of any of the chains of the protein
  • View the citation in which the structure was first characterized

In order to view structures, you must install the Cn3D software on your computer.  It is a free download from NCBI.  You can access the download page from http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml and follow the installation instructions. 

Once you have Cn3D installed, you can open and view the crystal structure for your protein by clicking on the button View 3D Structure on any structure page.  This will open a pop-up window that asks you to choose the program to open the molecule, with Cn3D as the default.  Click OK

This will open the molecule in a new window, laid over your MMDB structure page:

 

Cn3D view

 

 

Updated: November 27th, 2012 05:40


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