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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
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