BSA1
Homework for 1/12/2005
A
Do exercise 2.1, 2.4, 2.5, 2.6 and 2.8 in the book.
Comment to exercise 2.6: For the one-to-one relationship to be true,
there is an additional requirement on the alignments. Which?
B
Continue the exercise on dynamic programming in a spreadsheet. Make a
global alignment of these two sequences:
GHGKKVADALTN
GHKRLLT
Use BLOSUM 50 and a linear gap penalty of 8.
First calculate the DP matrix as in the exercise. Then make a table
with backtrack information. It could show a "u" or an up arrow for
"up", a "d" or "\" for diagonal and "l" or left arrow for the left
cell. You can use the IF function in the spreadsheet to select the
right cell. It is easiest if it is a separate table.
Deduce the alignment manually - or automatically if you want (I
have no idea how to do it).
C
Now change the spreadsheet to do local alignment of the two sequences
above. Use the same parameters as above (BLOSUM50 and linear gap
penalty of 8).
For B and C:
Write the alignment and the total score in the answer to the exercise.
Attach the spreadsheet(s) in electronic form, so I can see the
formulas.
Send your work to krogh at binf.ku.dk
Please use this subject:
BSA1
homework 1
Anders Krogh, Nov. 20, 2005