| 1 | Install and run this Perl implementation of the Needleman and Wunsch algorithm [nw] in order to align these two sequences: A and B. Examine the code to figure out how the sequences should be provided to the program |
| Solution:./nw.pl seq1.fasta seq2.fasta |
| 2 | What is the cost for a substitution? an Indel?. Modify the scoring scheme so that the program produces this alignment:
THEBIGCAT
THER---AT |
| Solution: [nw_2] |
| 3 | Modify the code so that it prints out the score of the alignment |
| Solution: [nw_3] |
| 4 | Modify the recursion so that INDELS get different penalties in sequence A and B |
| Solution: [nw_4] |
| 5 | Modify the recursion so that the alignment becomes local (Smith and Waterman) |
| Solution: [sw] |