Using Biology Workbench for Students

 

  1. To set up an account, go to http://www.inquiry.uiuc.edu/bioweb/perl/register.html  and follow the instructions.

 

  1. If you already have an account, go to http://www.inquiry.uiuc.edu/bioweb/perl/bioweb.cgi

 

  1. Enter 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.

 

  1. The first thing you need to do is get some protein sequences to work with.  Click on the Ndjinn to perform a search.

 

  1. Choose 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.

 

  1. Scroll down and type the protein that you are looking for into the search box.  Be specific!  The databases are HUGE!  Then click Submit.

 

  1. This 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.

 

  1. This 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.

 

  1. After 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.

 

  1. Enter your username and password when prompted.

 

  1. This 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.

 

  1. If you scroll down farther you will se an ěunrooted treeî which shows the likely evolutionary relationships among the proteins.

 

  1. Below the ěunrooted treeî, click Import alignments.  This will take you to the Alignment Tools page.

 

  1. Scroll to the bottom of the page and choose the alignment you would like to work with.

 

  1. Scroll back to the top of the page and click on the Drawgram button to create a ěrooted treeî.

 

  1. The 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.

 

  1. To find closely related proteins, select ONE protein from your workbench and click the BLASTP button.

 

  1. Choose a database (SwissProt works well) by clicking in the white circles.  Then scroll down and click Submit.

 

  1. Scroll down and you will see a list of up to 1000 related proteins.

 

  1. Select the sequences you want and click the Import Sequences button.

 

  1. You can now use the new sequences for any of the functions described above.

 

Amino Acid Codes                            Codon

A                     Alanine                        GCU GCC GCA GCG                       Stop codons

C                     Cysteine                      UGU UGC                                     UAA UAG UGA

D                     Aspartic Acid             GAU GAC

E                      Glutamic Acid             GAG GAA

F                      Phenylalanine              UUU UUC

G                     Glycine                       GGG GGU GGC GGA

H                     Histidine                     CAU CAC

I                       Isoleucine                    AUU AUC AUA

K                     Lysine                         AAA AAG

L                      Leucine                        UUA UUG CUU CUC CUA CUG

M                    Methionine                 AUG  (start)

N                     Asparagine                  AAU AAC

P                      Proline                         CCU CCC CCA CCG

Q                     Glutamine                   CAA CAG

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 UAC