Alignment Engine

The tool implements affine gap dynamic programming.

Gap Model

  • GAP_OPEN = -5
  • GAP_EXTEND = -1

States

  • S: match/mismatch
  • E: gap in X
  • F: gap in Y

Recurrence

Each cell considers:

  • Match/mismatch
  • Gap open
  • Gap extension

Modes

  • Global (Needleman–Wunsch)
  • Local (Smith–Waterman)

Local alignment resets negative scores to zero.

Traceback

  • Encoded via pointer matrix
  • Supports reconstruction of alignment path