Selecting a Protein Data Set:
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.