REPuter

REPuter detects and analyzes repetitive DNA structures in genomic and inter-genomic sequences to identify repeat types and assess their biological significance.

Key Features:

• Efficient Detection: Detects a wide array of repeat types within genomic DNA to provide comprehensive coverage across genomes.
• Significance Evaluation: Evaluates the significance of identified repeats to help distinguish biologically relevant repeats from artifacts.
• Interactive Visualization: Provides interactive visualization of repeat structures to aid interpretation of genomic repeat architecture.

Scientific Applications:

• Fragment Assemblies: Checks fragment assemblies by identifying repeat structures that may complicate or inform assembly processes.
• Low Copy Repeats Search: Searches for low copy repeats relevant to genomic stability and variation.
• Unique Sequence Identification: Identifies unique sequences amidst repetitive DNA to delineate regions of interest.
• Gene Structure Comparison: Facilitates comparison of gene structures across genomes or within a single genome to study conservation and divergence.
• cDNA/EST Mapping: Maps cDNA and EST sequences to genomic DNA to support annotation and analysis of expressed genes.

Methodology:

Performs algorithmic detection of repeat types, evaluates repeat significance, and visualizes repeat structures.