Biovisualization Datasets Page
Links to datasets for Project 2 (making trees).
Links to datasets for Project 3 (experimental results).
Links to datasets for Project 4 (Sequences).
Links to datasets for Project 5 (3D structures).
Swiss-Prot is a good source of protein sequences. You just need to
go to the List of Entries and type in the name of a protein in the Query
field, then Search. Scroll down to the Sequence, and click on FASTA.
You can find a few short ones for display and alignment here:
DUT_BUCAI . Once you find a protein you
like (e.g., DUT_BUCAI), you can get the DNA sequence
for it by going to Cross-ref, and then click on GenBank and the
sequence ID to the right. You can then request FASTA format, and Send it
to a file, such as: sample DNA . Note
you will get the entire sequence, not just the section corresponding to the
Protein interaction database tool. You can generate data for 3D graphs
by going to this site, choosing one of the example proteins, and hit GO. This
will generate a graph, which you can make larger (by hitting +) or smaller (by
hitting -). Note that it supports links found via many different methods.
You can then get the table of links and link scores by going to Save and scroll
down to the Text Summary option. This gives you a tab-separated file with
one row per link and the strength of each link via 8 or 9 different measures.
Some examples (after removing the unnecessary columns) can be found
This describes the format for 3D molecular models in XYZ format. You can
convert molecular models of other formats into XYZ using
this tool . Some examples are