Perform pairwise global (Needleman-Wunsch) or local (Smith-Waterman) sequence alignment with configurable match, mismatch, and gap penalty scores. Use this tool to compare a newly sequenced gene against a reference, identify conserved domains between homologous proteins, or check primer specificity against off-target templates. The alignment output shows matching residues, gap positions, and percent identity — the dynamic programming matrix with traceback path is also available for understanding how the algorithm arrives at the optimal alignment.

Features

• Global Alignment: Needleman-Wunsch algorithm for full sequence alignment
• Local Alignment: Smith-Waterman algorithm for local similarity detection
• Configurable Scoring: Adjustable match, mismatch, and gap penalty scores
• DNA & Protein: Auto-detection with BLOSUM62 scoring for proteins
• DP Matrix: Visualize the dynamic programming matrix with traceback path
• Identity & Similarity: Calculate sequence identity and similarity percentages