Now you should leave the computer and make sure you understand
how dynamic programming for sequence alignments work.
Longest common substring
Determine the LCS of the following sequences X={A,B,D,C,D,B,C,D}
and Y={B,D,D,B,D,C,D}
Determine the LCS of the following sequences X={1,0,0,1,0,1,0,1}
and Y={0,1,0,1,1,0,1,1,0}
Simple examples
We have the following sequences:
AKWIL and AWLI how do they align using:
Local alignments with an identity matrix and no gap penalties
Global alignments with an identity matrix and no gap penalties
Local alignments with Blossum62 and no gap penalties
Global alignments with Blossum62 and no gap penalties
Local alignments with Blossum62 and gap penalties -10,-1
Global alignments with Blossum62 and gap penalties -10,-1
Example of real sequences
Azurin (2aza) and plastocyanin (2pcy ) are related. You should use the
Blossum62 matrix and calculate the alignment of the first 10
residues of these two sequences using the blossom62 substitution
matrix and the gap penalties, -1 and -10. You should try both local
and global alignments.
In the lab report you should show the alignment and alignment
matrix (including arrows).
Resources
However if you do want to use a computer there are some nice tools available:
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