NCBI Tutorial Notes BSCI 410 Spring 09/Liu
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Ch 5: OMIM (Online Mendelian Inheritance in Man)
Click on statistics on the left (under OMIM facts)
A Table shows all the genes entered in OMIM (about half of the 35,000 human
genes are shown)
Click on X-linked
Click on the first entry-get the description about the gene
Go back to OMIM, Click on Update Log (just below Statistics)
See the record is updated every month
Go back to OMIM, enter "Huntington" in the search window-Go
You will get 112 entries
Click on the first entry (OMIM number *143100)
See the wealth of info on this disease
Click on Map "4p16.3" -get a table- click 4p16.3 in the top of table
By zooming in on the locus (use the zoom in feature just above the
chromosome graphic on the very left), we can display the genes that are located
close to the Huntington locus. Under the Morbid column are various loci associated
with disease phenotypes.
Click on HD line the "3064"
Led to Entrez Gene record for the Huntington disease gene with links
to many information resources
Click HGMD (the human genetic diseases database) on the right under LINK.
HGMD is specializing in the nature of characterized mutations for various loci.
Note the trinucleotide repeat for HD (now need registration/password-)
Go back to Entrez Gene, click 'SNP" on the right column
Click Gene structure (a box appear to allow you to select FASTA)
Click "see HD in Mapview"
Ch 6: Structure (Click on Structure at the top black bar of the NCBI homepage)
Structural databases such as Entrez Structure at NCBI contain details of protein
structure based on X-ray crystallographic and NMR studies. From this database it is
possible to retrieve and examine a particular three-dimensional structure in a viewer
called Cn3D. In this tutorial, we will examine some structures and learn to use the
Cn3D structural viewer.
Download Cn3D v4.1 by clicking on Cn3D v4.1 on the left-hand side menu.
Type 1JM6 (the ID for rat pyruvate dehydrogenase in the PDB protein
database)-Click Go.
When the result appears, click 1JM6 to see the NCBI Molecular Modeling
Database (MMDB) Structure Summary page (NCBI's structure database is called
MMDB (Molecular Modeling DataBase), and it is a subset of three-dimensional structures
obtained from the Protein Data Bank (PDB), excluding theoretical models.)
Click "View 3D Structure"
You will see alpha helices are shown as green cylinders and beta pleated sheets
as gold flat arrows. The connecting amino acid chain is in blue.
Use your mouse to drag the molecule and rotate it. Note that it consists of two
mirror image complexes consisting of the A and B chains. Notice the bound ADP
molecule in each complex (partly colored in red and complexed with a Mg ion)? Can you
