Using Biology Workbench for Students
- To set
up an account, go to http://www.inquiry.uiuc.edu/bioweb/perl/register.html and follow the instructions.
- If you
already have an account, go to http://www.inquiry.uiuc.edu/bioweb/perl/bioweb.cgi
your user name and password.
This should take you to the Protein Tools page.
If not, click on the Protein Tools button on the left side of the page.
first thing you need to do is get some protein sequences to work
with. Click on the Ndjinn to perform a search.
the database you wish to use by clicking in the white boxes to select or
deselect databases. If you
are looking for a protein sequence from various animals, PIR is a good choice. If you are looking for a protein sequence from a virus GBVRL is a good choice.
down and type the protein that you are looking for into the search
box. Be specific! The databases are HUGE! Then click Submit.
gives you a list of matches.
To select several sequences at once, press and hold the Ctrl or
Apple key while you click
on the matches you want with your mouse. Then scroll down and click Import Sequences.
Do not try to import more than 60 sequences at once. Biology Workbench may crash.
takes you back to the Protein Tools page. If you scroll down, the sequences
you just imported will be listed under ěProtein sequencesî. Choose the proteins you want to
compare by clicking the white boxes.
you have selected your proteins, scroll to the top of the page. We are now going to compare the
protein sequences by clicking on CLUSTALW.
your username and password when prompted.
page displays the amino acid sequences for the selected proteins. Amino acids that are the same for
all of the proteins (were conserved) will appear bright blue. Those that are mostly the same
appear green. Those that were
somewhat the same appear dull or dark blue. Amino acids that vary too much for the computer to be
able to find similarity will appear black.
- If you
scroll down farther you will se an ěunrooted treeî which shows the likely
evolutionary relationships among the proteins.
the ěunrooted treeî, click Import alignments.
This will take you to the Alignment Tools page.
to the bottom of the page and choose the alignment you would like to work
back to the top of the page and click on the Drawgram button to create a ěrooted treeî.
rooted tree will show you the inferred (from the data available)
evolutionary relationships of the proteins as compared to a common
ancestor. The length of the
line indicates relative evolutionary distance from the common ancestor.
find closely related proteins, select ONE protein from your workbench and
click the BLASTP button.
a database (SwissProt works well) by clicking in the white circles. Then scroll down and click Submit.
down and you will see a list of up to 1000 related proteins.
the sequences you want and click the Import Sequences button.
can now use the new sequences for any of the functions described above.
Amino Acid Codes Codon
A Alanine GCU
GCC GCA GCG Stop
C Cysteine UGU
F Phenylalanine UUU
G Glycine GGG
GGU GGC GGA
H Histidine CAU
I Isoleucine AUU
K Lysine AAA
L Leucine UUA
UUG CUU CUC CUA CUG
M Methionine AUG (start)
N Asparagine AAU
P Proline CCU
CCC CCA CCG
Q Glutamine CAA
R Arginine AGA
AGG CGU CGC CGA CGG
S Serine UCU
UCC UCA UCG AGU AGC
T Threonine ACU
ACC ACA ACG
V Valine GUU
GUC GUA GUG
W Tryptophan UGG
Y Tyrosine UAU