convert-matrix

convert-matrix converts between position-specific scoring matrix (PSSM) formats and computes position-specific and aggregate statistics to support motif analysis in regulatory sequence studies.

Key Features:

• Format Interconversion: Converts between different PSSM formats to enable compatibility across bioinformatics workflows and databases.
• Position-specific Statistics: Computes position-specific scores including weights, frequencies, and information content for each matrix column.
• Aggregate Statistics: Calculates marginal frequencies and total information content to summarize motif properties across the matrix.
• Consensus Generation: Produces strict and degenerate consensus sequences derived from PSSMs for motif representation.
• P-value Estimation: Supports P-value calculation using adaptive background models and Markov-chain estimation.
• Integration with RSAT: Operates as part of the Regulatory Sequence Analysis Tools (RSAT) suite for regulatory sequence analysis.

Scientific Applications:

• Cis-regulatory element detection: Enables conversion and analysis of PSSMs to assist in identifying potential cis-regulatory sites.
• Pattern Discovery: Assists identification of conserved sequence motifs across species or experimental conditions.
• Phylogenetic Footprinting: Aids detection of evolutionarily conserved regulatory elements through analysis of aligned sequences.
• Genome Scanning and Feature Mapping: Supports genome-wide scans to locate and annotate potential regulatory sites.

Methodology:

Computes position-specific scores (weights, frequencies, information content) and general statistics (marginal frequencies, total information content); uses adaptive background models and Markov-chain estimation for P-value calculation.