Amino Acid Sequence Comparison  

Angelique Bosse
Montgomery Blair High School
Silver Spring, Maryland 20901

  • Go to Biology Workbench at
  • Click "Enter the Biology Workbench 3.2" and enter user name and password, click "ok" (or set up a free account first)
  • Scroll down and click "Protein Tools"
  • Select "Ndjinn- Multiple Database Search"
  • Click "Run"
  • In the skinny white box next to "Exact Match" type in a protein such as " beta hemoglobin" and select "Show 10 Hits"
  • Scroll down to choose a database such as "SWISSPROT- Swissprot Database" by clicking in white box
  • Go back up to top of screen and click "Search"
  • Result is a list of "hits" for your requested protein under "Matching Database Record".
  • Select two unrelated species (such as human and rabbit) by clearing the little white boxes next to all EXCEPT your selections (only the white boxes next to chick and bovine should have check marks)
  • Click "Import Sequence(s)"
  • From the menu list, scroll down and select "CLUSTALW- Multiple Sequence Alignment"
  • Click the boxes next to your two imported sequences
  • Click "Run"
  • On the next screen click "Submit"
  • Result is alignment of your two chosen sequences
  • Above the aligned sequence is a "consensus key" showing what each of the symbols means. The amino acids are classified as fully conserved, strongly conserved, weakly conserved, or no consensus.
  • Click "Import Alignments"
  • From the menu, click "BOXSHADE- Color-Coded Plots of Pre-Aligned Sequences"
  • Click white box next to "CLUSTALW" protein and your two imported sequences
  • Click "Run"
  • On the next screen click "Submit"
  • Scroll down to see color-coded plot of your sequence alignment
    • green = identical
    • blue = similar
    • gray = different
  • Click "Return"

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