DNA Sequence Alignment

Perform global alignment of two DNA sequences using Needleman-Wunsch algorithm

Input Sequences
bp
Needleman-Wunsch Algorithm
Global DNA sequence alignment method and interpretation guide

What is Sequence Alignment?

Global alignment of DNA sequences using the Needleman-Wunsch algorithm, which aligns the entire length of both sequences from start to finish. This method is particularly useful for comparing sequences of similar length and understanding their evolutionary relationship.

Result Metrics

Identity (%)

Percentage of bases that match exactly. Higher values indicate greater sequence similarity.

Alignment Score

Total score calculated based on matches, mismatches, and gaps. Higher scores indicate better alignment quality.

Mismatches

Positions where bases differ, indicating point mutations or sequence variations.

Gaps

Inserted or deleted bases representing indel mutations.

Scoring Matrix: EDNAFULL

Match (identical bases):+5
Mismatch (different bases):-4
Gap (insertion/deletion):-2

Visualization Colors

Match: Identical bases
Mismatch: Different bases
Gap: Insertion or deletion

Input Format

Accepts FASTA or raw sequence format:

  • Auto-converts to uppercase
  • Removes whitespace
  • Replaces invalid chars with 'N'