CloneSet308

Bio/pairwise2.py

Bio/pairwise2.py

        # Align the first residue in sequenceB to the ith residue in
        # sequence A.  This is like opening up i gaps at the beginning
        # of sequence B.
        score = match_fn(sequenceA[i],sequenceB[0]) 
        if penalize_end_gaps: 
             score+=gap_B_fn(0,i) 
        score_matrix[i][0] = score 

        score = match_fn(sequenceA[0],sequenceB[i]) 
        if penalize_end_gaps: 
             score+=gap_A_fn(0,i) 
        score_matrix[0][i] = score 


        # Fill in the score matrix.  Each position in the matrix
        # represents an alignment between a character from sequenceA to
        # one in sequence B.  As I iterate through the matrix, find the
        # alignment by choose the best of:
        #    1) extending a previous alignment without gaps
        #    2) adding a gap in sequenceA
        #    3) adding a gap in sequenceB

  # Align the first residue in sequenceB to the ith residue in
  # sequence A.  This is like opening up i gaps at the beginning
  # of sequence B.
  score = match_fn(sequenceA[ [[#variable31a0da20]]],sequenceB[ [[#variable31a0d9c0]]]) 
  if penalize_end_gaps:
  
    score+= [[#variable31a0d940]](0,i) 
  score_matrix[ [[#variable31a0da20]]][ [[#variable31a0d9c0]]] = score 
  # Fill in the score matrix.  Each position in the matrix
  # represents an alignment between a character from sequenceA to
  # one in sequence B.  As I iterate through the matrix, find the
  # alignment by choose the best of:
  #    1) extending a previous alignment without gaps
  #    2) adding a gap in sequenceA
  #    3) adding a gap in sequenceB
 

i 

0 

0 

i 

gap_B_fn 

gap_A_fn