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Sequence Alignment

Perform global or local alignment between two sequences.

How to Use

Global Alignment (Needleman-Wunsch)

Best for aligning sequences of roughly equal length from end-to-end. It attempts to match every residuary in both sequences.

  • Use case: Comparing homologous genes or proteins.
  • Algorithm: Maximizes the total score of the alignment matrix.

Local Alignment (Smith-Waterman)

Finds the most similar region (substring) between two sequences. Useful for finding motifs or domains within larger sequences.

  • Use case: Finding a gene in a genome or a domain in a protein.
  • Algorithm: Allows the alignment to start and end anywhere.