MoSDi

MoSDi performs probabilistic analysis using Probabilistic Arithmetic Automata (PAAs) to compute distributions arising from operations whose operands are governed by stochastic processes for applications in computational biology.

Key Features:

• Probabilistic Arithmetic Automata (PAA) framework: Describes chains of operations with probabilistically determined operands to model stochastic aspects of biological sequences and processes.
• Numerical computation algorithms: Computes distributions resulting from probabilistic calculations for quantitative analysis of statistical properties.
• Deterministic Arithmetic Automata (DAA): Models deterministic operations on sequences as a basis for constructing PAAs when combined with finite-memory random text models.

Scientific Applications:

• Pattern matching statistics: Computes distributions of occurrence counts, waiting times, and clump sizes in random texts under hidden Markov background models.
• Window-based pattern matching algorithms: Provides exact analysis of window-based pattern matching algorithm behavior on random texts.
• Sensitivity analysis of filtration seeds: Assesses sensitivity of filtration seeds used to detect candidate sequence alignments.
• Peptide fragment statistics: Calculates length and mass statistics of peptide fragments produced by enzymatic cleavage reactions.
• Sequencing read length statistics: Computes read length distributions for sequencing technologies such as 454 and IonTorrent.

Methodology:

Construct PAAs from DAAs using a finite-memory random text model.