text: user6469: I have a bioinformatics exam coming up. I can understand the difference between the global algorithm and the local algorithm, but I have a problem with gap opening penalty and gap extension penalty. What is the difference between gap opening penalty and gap extension? 
  Can anybody help me in working out how to use the gap opening penalty and gap extension penalty for blosum62?
  There are a lot of questions like the one below:
  Compute the score of the following sequence alignment given the BLOSUM62 matrix below and gap opening penalty (GOP) = 12, and gap extension penalty (GEP) = 2.
  SDRVIKAAIFDPIQPDF---G-----PVYFGLGHVH
  RDLVERLFILDMI-PGLIKAGDSFPIPVALMINHIF
  
     A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V
  A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0
  R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3
  N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3
  D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3
  C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1
  Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2
  E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2
  G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3
  H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3
  I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3
  L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1
  K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2
  M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1
  F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1
  P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2
  S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2
  T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0
  W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3
  Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1
  V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4
  
  
  user3818: Your alignment is 
  
  SDRVIKAAIFDPIQPDF---G-----PVYFGLGHVH
  RDLVERLFILDMI-PGLIKAGDSFPIPVALMINHIF
  
  For each position in the alignment you calculate the score for that alignment. For position 1 we'd look up S vs R in the matrix and find a score of -1. You continue doing this until you hit the first -, which is not in the matrix. The first - is a gapopening, each consequent - in a series of -'s counts as a gap extension, instead of an opening.
  ---G--
  IKAGDS
  
  gives
  -12 -2 -2 6 -12 -2
  
original_text: 6469: <p>I have a bioinformatics exam coming up. I can understand the difference between the global algorithm and the local algorithm, but I have a problem with gap opening penalty and gap extension penalty. What is the difference between gap opening penalty and gap extension? </p>
  
  <p>Can anybody help me in working out how to use the gap opening penalty and gap extension penalty for blosum62?</p>
  
  <p>There are a lot of questions like the one below:</p>
  
  <p><em>Compute the score of the following sequence alignment given the BLOSUM62 matrix below and gap opening penalty (GOP) = 12, and gap extension penalty (GEP) = 2.</em></p>
  
  <pre><code>SDRVIKAAIFDPIQPDF---G-----PVYFGLGHVH
  RDLVERLFILDMI-PGLIKAGDSFPIPVALMINHIF
  
     A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V
  A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0
  R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3
  N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3
  D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3
  C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1
  Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2
  E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2
  G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3
  H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3
  I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3
  L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1
  K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2
  M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1
  F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1
  P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2
  S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2
  T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0
  W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3
  Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1
  V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4
  </code></pre>
   3818: <p>Your alignment is </p>
  
  <p><code>
  SDRVIKAAIFDPIQPDF---G-----PVYFGLGHVH
  RDLVERLFILDMI-PGLIKAGDSFPIPVALMINHIF
  </code></p>
  
  <p>For each position in the alignment you calculate the score for that alignment. For position 1 we'd look up S vs R in the matrix and find a score of -1. You continue doing this until you hit the first -, which is not in the matrix. The first - is a gapopening, each consequent - in a series of -'s counts as a gap extension, instead of an opening.</p>
  
  <p><code>---G--
  IKAGDS
  </code>
  gives
  <code>-12 -2 -2 6 -12 -2</code></p>
  