Selecting a Protein Data Set:

Created by George Rice, Montana State University and Gretchen A. Koch, Goucher College.

Biology WorkBench Icon

Create a New Account In Biology WorkBench -

Start a New Protein Session

  • After starting a new session hit run and label it in the Session Description then click Start New Session.
  • In the new session click Protein Tools and highlight Ndjinn - Multiple Database Search.
  • Select a protein database such as "Swisprot" and click search.
  • Pick a protein of interest and click Import Sequences.
  • Find sequences that are similar to the one just selected by highlighting TBLASTN and clicking run.
  • Highlight a database (GenBank Bacterial Sequences) and change the 1-line descriptions to 5000, then click Submit Sequences at the bottom of the page.

Create Phylogenetic Tree in CLUSTALW -

  • Check all proteins in your data set and highlight CLUSTALW then hit run.
  • Now select Rooted and Unrooted Trees, select Run As Batch then hit submit.
  • Deselect all of the proteins, highlight Retrieve BATCH Output, then run.
  • Highlight your Batch Job, View Outputs, and Import Alignments.
  • Check CLUSTALW Protein on the left, highlight DRAWTREE, then run, and Submit on the next screen.
  • Click on image for larger file - 


  • Check CLUSTALW Protein on the left, highlight CLUSTALDIST, then run, and Submit on the next screen.
  • Highlight the distance matrix and import into MATLAB.