Perform optimal global alignment of two DNA sequences using a match/mismatch scoring matrix and configurable gap penalties.
Paste the first DNA sequence (FASTA or raw). Only A, C, G, T/U are retained (limit 20,000 characters).
Paste the second DNA sequence (FASTA or raw). Only A, C, G, T/U are retained (limit 20,000 characters).
Score for matching bases.
Score for mismatched bases.
Penalty applied to gaps preceding a sequence.
Penalty applied to internal gaps.
Penalty applied to gaps following a sequence.
Paste two DNA sequences in FASTA or raw format. Only A, C, G, T/U characters are retained (limit 20,000 characters per sequence).
Set match score (reward for identical bases) and mismatch score (penalty for different bases). Typical values are +2 for matches and -1 for mismatches.
Configure leading, internal, and trailing gap penalties. Setting leading/trailing to 0 allows free gaps at sequence ends (common for global alignment).
The Needleman-Wunsch algorithm produces an optimal global alignment with gaps marked by dashes. The alignment score reflects match/mismatch scores and gap penalties.
The match score is added when aligned bases are identical. The mismatch score (typically negative) is added when bases differ. Adjust these values to control the sensitivity of the alignment.
This tool uses the Needleman-Wunsch algorithm to compute the optimal global alignment. The alignment score reflects the sum of all match, mismatch, and gap penalties.