Introduction to Sequence Alignment

• Sequence alignment is the process of arranging two or more sequences to identify similarities and differences.
• Alignment helps in studying evolutionary relationships, identifying conserved regions, and detecting mutations.

Types of Sequence Alignment

1. Pairwise Alignment:

   • Aligns two sequences to identify similarities and differences.
   • Common algorithms: Needleman-Wunsch, Smith-Waterman.

2. Multiple Sequence Alignment (MSA):

   • Aligns multiple sequences simultaneously.
   • Common algorithms: ClustalW, MUSCLE.

Pairwise Alignment

from Bio import pairwise2
from Bio.Seq import Seq

sequence1 = Seq("ACGTGATCGT")
sequence2 = Seq("ACGTCATCGT")

alignments = pairwise2.align.globalxx(sequence1, sequence2)

for alignment in alignments:
    print("Alignment Score:", alignment[2])
    print("Aligned Sequence 1:", alignment[0])
    print("Aligned Sequence 2:", alignment[1])
    print()

• Import the necessary modules from Biopython.
• Define two sequences to align.
• Perform global pairwise alignment using pairwise2.align.globalxx() function.
• Iterate over the alignments and print the alignment score and aligned sequences.

Multiple Sequence Alignment

from Bio import Align

sequences = [
    "ACGTGATCGT",
    "ACGTCATCGT",
    "ACGTTATCGT"
]

aligner = Align.PairwiseAligner()
aligner.mode = "global"

alignment = aligner.align(sequences)

for aligned in alignment:
    print(aligned)