After this practical you will be able to:
Copy the example programs from directory
/chalmers/users/kemp/TDA507/practical1 (also available
online).
Compile and run these programs.
Modify the program global_alignment.c (or GlobalAlignment.java) so that an extra line of output is printed between the two aligned sequence, indicating exact matches with the character "|", e.g.
AT-CGAT || || | ATACG-T
Modify the program global_alignment.c (or GlobalAlignment.java) so that
the percent identity between the two sequences is written out.
Add a comment to your program explaining how you have decided
to calculate the percent identity.
Modify the program global_alignment.c (or GlobalAlignment.java) to output the Hamming distance between the aligned sequence strings.
Copy the program global_alignment.c (or GlobalAlignment.java) to the file
local_alignment.c (or LocalAlignment.java).
Modify this program so that it implements the Smith-Waterman algorithm
for finding an optimal local alignment.
Test your program with the sequences "PAWHEAE" and "HDAGAWGHEQ".
Check your results with the
online program.
Copy the program global_alignment.c (or GlobalAlignment.java) to the file levenshtein.c (or Levenshtein.java). Modify this program so that it calculates the Levenshtein distance (the edit distance) between the two sequenceis.
Modify the program global_alignment.c (or GlobalAlignment.java) so that it
counts the total number of optimal alignments for the two sequences.
Test your program with the sequences "ATTA" and "ATTTTA".
Modify the program global_alignment.c (or GlobalAlignment.java) so that it writes out all of the optimal alignments for the two sequences.
You should submit your solutions via the Fire system.
Everyone should do questions 1, 2, 3 and 4. Those aiming for a higher grade should also attempt questions 5, 6 and 7.
Test your programs with suitable test data. Upload the following to the Fire system:
global_alignment.c (or GlobalAlignment.java)
local_alignment.c (or LocalAlignment.java)
levenshtein.c (or Levenshtein.java)
A (plain text or PDF) file that shows the result of compiling and running your programs.