Scoring Matrix Calculator

Calculate protein alignment scores using BLOSUM and PAM substitution matrices. Visualize amino acid substitution penalties.

Total Score
0
Identities
0%
Positives
0%
Matrix Used
BLOSUM62

Substitution Matrix Heatmap

What are Scoring Matrices?

Scoring matrices (substitution matrices) quantify the likelihood of amino acid substitutions in evolution. BLOSUM matrices are based on observed substitutions in conserved protein blocks, while PAM matrices model evolutionary distances.

How to Use This Calculator

Calculate alignment scores step by step:

  1. Choose a scoring matrix (BLOSUM62 is standard)
  2. Enter two protein sequences to compare
  3. View position-by-position scores
  4. Compare results across different matrices

When to Use Different Matrices

Choose matrices based on sequence similarity:

  • BLOSUM80: Closely related sequences (>80% identity)
  • BLOSUM62: Standard for most alignments
  • BLOSUM45: Distantly related sequences
  • PAM250: Very divergent sequences

Example Input

Hemoglobin alpha chains:

Seq1: MVHLTPEEKSAVTAL
Seq2: MVHLTDAEKSAATAL

Try the Example button for a full comparison.

Understanding Scores

Score interpretation:

  • Positive scores: Favorable substitutions
  • Zero: Neutral substitutions
  • Negative scores: Unfavorable substitutions
  • Diagonal values: Identity scores

FAQ

Q: Why are some substitutions positive?
A: Similar amino acids (e.g., K↔R) often substitute without affecting protein function.

Q: Which matrix should I use?
A: BLOSUM62 is the default for most protein comparisons. Use BLOSUM80 for very similar sequences.