Sequence alignment algorithm

Gotoh Local Alignment

Classical gotoh local algorithm

In [1]: import seq_aligner

In [2]: r=seq_aligner.gotoh_local_align("CCAGCT", "AGCCTA", 1,-1,-3,-1)

In [3]: seq_aligner.print_align_map(r[0],r[1][0])
3     AGC     5 Score:3
      |||      
1     AGC     3

Gotoh Semi-Global Alignment

Classical gotoh semi-global algorithm.
Initialize the top row and leftmost column to zero and terminate end at either the bottom row or rightmost column [ref].

In [4]: r=seq_aligner.gotoh_semi_global_align("CCAGCT", "AGCCTA", 1,-1,-3,-1)

In [5]: seq_aligner.print_align_map(r[0],r[1][0])
3     AGCT     6        Score:2
      |||*      
1     AGCC     4

Gotoh Local Global Alignment

Variants of the local and semi-global algorithms

In [6]: r=seq_aligner.gotoh_local_global_align("CCAGCT", "AGCCTA", 1,-1,-3,-1)

In [7]: seq_aligner.print_align_map(r[0],r[1][0])
3     AGC---     5      Score:-3
      |||         
1     AGCCTA     6