How to Calculate Pairwise Sequence Alignment?

You can use the Bio.Align.PairwiseAligner() function to Calculate Pairwise Sequence Alignment. It uses the Needleman-Wunsch, Smith-Waterman, Gotoh (three-state), and Waterman-Smith-Beyer global and local pairwise alignment algorithms.

Here is an example on how to calculate the alignment score using the score() function.

fyicenter$ python
>>> from Bio import Align
>>> aligner = Align.PairwiseAligner()
>>> score = aligner.score("GAACT", "GAT")
>>> score
3.0

You can also use the align() function to see how two sequences can be aligned.

>>> alignments = aligner.align("GAACT", "GAT")
>>> for alignment in alignments:
...   print(alignment)
... 
target            0 GAACT 5
                  0 ||--| 5
query             0 GA--T 3

target            0 GAACT 5
                  0 |-|-| 5
query             0 G-A-T 3

The output shows 2 alignments (2 ways to align the given 2 sequences).

In both alignments, the alignment score is 3.0, which calculated with 2 default scoring rules:

• Any matched letter pair gets 1.0 additional score.
• Any mismatched letter pair gets 0.0 additional score.
• Any gap gets 0.0 additional score.

For example, the following Pairwise Sequence Alignment will get a score of 3.0.

target            0 G A A C T 5
                  0 | | - - | 5
query             0 G A - - T 3
                    ---------
score               1 1 0 0 1 = 3.0

⇒ Pairwise Sequence Alignment Score Settings

⇐ Parse PDB Entry with Bio.PDB.MMCIFParser.parser Module

⇑ Biopython - Tools for Biological Computation

⇑⇑ OBF (Open Bioinformatics Foundation) Tools