PairwiseStatSig

PairwiseStatSig estimates the pairwise statistical significance of local alignments between two protein sequences using censored Maximum Likelihood Fitting to model alignment score distributions for homology assessment.

Key Features:

• Database Independence: Estimates statistical significance without requiring external sequence databases.
• Censored Maximum Likelihood Fitting: Applies censored Maximum Likelihood Fitting to model the distribution of alignment scores.
• Multiple Parameter Sets: Supports multiple alignment parameter sets while maintaining homology detection performance.
• Parameter Set Change Penalty: Incorporates a penalty for changing parameter sets during alignment scoring.
• Extreme Value Distribution Assumption: Operates under the assumption that alignment score distributions follow an extreme value distribution.

Scientific Applications:

• Evolutionary relationship inference: Assess evolutionary relationships between protein sequences using pairwise local alignment significance.
• Homology hypothesis validation: Validate hypotheses about sequence homology by quantifying alignment significance independent of database searches.
• Alignment parameter optimization: Optimize and evaluate alignment parameter settings using support for multiple parameter sets and change penalties.

Methodology:

Uses censored Maximum Likelihood Fitting to model the distribution of local alignment scores, supports multiple parameter sets with a parameter-set change penalty, and relies on the assumption that alignment score distributions follow an extreme value distribution.