CorGen

CorGen measures long-range correlations in DNA GC-content and generates random DNA sequences that preserve those correlation parameters for use as null models in computational genomics.

Key Features:

• Measurement and Analysis: Quantifies long-range correlations in base composition, with explicit analysis of GC-content autocorrelation and its power-law decay behavior.
• Random Sequence Generation: Produces random DNA sequences that maintain the same correlation parameters as the input sequence or user-specified parameters for use as correlated null models.
• Expansion-Randomization Dynamics: Implements an expansion–randomization dynamics algorithm to generate sequences with specified long-range correlation structure.

Scientific Applications:

• Sequence Alignment: Accounts for long-range correlations to improve alignment score statistics and comparative genomic analyses.
• Motif Finding Algorithms: Incorporates long-range correlations into null models to improve the performance and precision of motif discovery.

Methodology:

Computes GC-content autocorrelation functions (noting power-law decay) and employs expansion–randomization dynamics to generate random sequences that preserve specified correlation parameters.