Target Frequency Analyzer

Analyze and compare target frequencies from scoring matrices to understand optimization

What is Target Frequency Analysis?

Target frequencies (q_ij) represent the probability of finding amino acid pairs in true alignments. Every scoring matrix implicitly optimizes for specific target frequencies through the formula: s_ij = log(q_ij / p_i p_j).

How to Use This Analyzer

Understand what your scoring matrix optimizes for:

  1. Select a scoring matrix to analyze
  2. Choose background frequency model
  3. View target frequencies and statistics

When to Use

This tool is useful when you need to:

  • Understand what a matrix is optimized for
  • Compare target frequencies between matrices
  • Design custom scoring matrices

Example Input

Matrix parameters:

Matrix: BLOSUM62
Background: Robinson-Robinson
Comparison: PAM250

Compare different matrices and backgrounds.

Example Output

Target frequency analysis:

q(W,W) = 0.0024 (2.4× expected)
q(C,C) = 0.0022 (11.7× expected)
Lambda = 0.2670 bits

Shows enrichment over background.

FAQ

Q: What are target frequencies?
A: They represent the probability of amino acid pairs in aligned homologous sequences.

Q: How do they relate to scores?
A: Scores are log-odds: s_ij = log(q_ij/p_ip_j), comparing target to background frequencies.