Identity and Similarity

Calculate identity and similarity between aligned DNA or protein sequences with substitution matrix analysis

Analysis Options

DNA/RNA
Protein
BLOSUM62
PAM250

Analysis Summary

What is Identity and Similarity?

Identity measures the percentage of exact matches between aligned sequences, while similarity considers biochemically similar amino acids. For proteins, substitution matrices like BLOSUM62 define which amino acids are considered similar based on evolutionary conservation.

How to Use This Identity Calculator

Quick analysis in three steps:

  1. Paste aligned sequences (must be same length with gaps)
  2. Select sequence type and matrix for proteins
  3. View detailed results with alignment visualization

When to Use

This tool is essential for:

  • Evaluating sequence alignment quality
  • Comparing homologous sequences from different species
  • Assessing protein functional conservation
  • Validating sequence similarity predictions

Example Input

Sample aligned sequences:

ATCG-TCGATCG
ATCGATCGA-CG

Sequences must be the same length including gaps (-).

Example Output

Analysis results include:

Identity: 83.3%
Similarity: 91.7%
Matches: 10/12
Gaps: 2

Visual alignment shows matches (*), gaps (-), and mismatches (.).

FAQ

Q: What's the difference between identity and similarity?
A: Identity counts exact matches only, while similarity includes biochemically similar amino acids.

Q: Do I need pre-aligned sequences?
A: Yes, sequences must be aligned and the same length including gaps.