Angelique Bosse
Montgomery Blair High School
Silver Spring, Maryland 20901
-
Go to Biology Workbench at http://workbench.sdsc.edu/
- 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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