Pair wise protein sequence
alignments can be very useful in determining conserved portions of a
protein. For example an active site is
likely to be highly conserved while other portions of the protein are less
likely to be conserved.
Instructions:
1. Obtain the protein
sequences that you wish compare.
2. Paste a sequence in
each of the two boxes
(There can be no spaces, numbers or headings in the sequence that is pasted, so delete spaces, numbers and headings if they are present).
3. Run the program
a.
To run a general alignment test chose “SIM” under “Chose Search Method.’
b.
Click on the “perform search” button.
c.
The results will give you information on the percent similarity of the two
proteins.
-OR-
a.
Another search method that is useful is the “LFASTA” option that identifies
local sequence alignments.
8. The Help menu found under [H] next to each of the Search Methods is useful if you get stuck or have additional questions.
When you are ready, click
here to start.
BCM Search Launcher: Pairwise Sequence Alignment