Pairwise Align Protein

Perform optimal global alignment of two protein sequences using configurable scoring matrices and gap penalties.

Tool Configuration
Configure the parameters for Pairwise Align Protein

Paste the first protein sequence (FASTA or raw). Only standard amino acids are retained (limit 20,000 characters).

Paste the second protein sequence (FASTA or raw). Only standard amino acids are retained (limit 20,000 characters).

Select the amino acid substitution matrix for alignment scoring.

Penalty applied to gaps preceding a sequence.

Penalty applied to internal gaps.

Penalty applied to gaps following a sequence.

1

Input Two Protein Sequences

Paste two protein sequences in FASTA or raw format. Only standard amino acid characters are retained (limit 20,000 characters per sequence).

2

Select Scoring Matrix

Choose PAM30/PAM70 for closely/moderately related sequences, BLOSUM62 for general purpose alignment, or BLOSUM45/BLOSUM80 for distant/closely related proteins.

3

Configure Gap Penalties

Set leading, internal, and trailing gap penalties. Internal gaps typically have higher penalties, while end gaps are often set to 0 for global alignment.

4

Analyze Alignment

Results show the optimal global alignment using the Needleman-Wunsch algorithm with your chosen matrix. Higher scores indicate better sequence similarity.

Scoring Matrices
Information about the available protein substitution matrices.

Matrix Selection

Different scoring matrices are optimized for different sequence divergence levels:

  • PAM (Point Accepted Mutation): PAM30 for closely related sequences, PAM70 for more distant sequences
  • BLOSUM (Blocks Substitution Matrix): BLOSUM80 for closely related, BLOSUM62 for general use, BLOSUM45 for distant sequences

Gap Penalties

This tool uses the Needleman-Wunsch algorithm to compute the optimal global alignment. You can adjust gap penalties to balance alignment quality with sequence conservation.