Asymmetron

Asymmetron identifies and analyzes DNA strand asymmetry patterns within biological sequences to investigate their impact on replication, transcription, and transcription factor binding.

Key Features:

• Strand Asymmetry Identification: Detects strand asymmetries across consecutive occurrences of single genomic elements and between pairs of overlapping or non-overlapping elements.
• Orientation Measurement: Measures strand asymmetries relative to both transcriptional and replicative orientations.
• Feature Orientation Assignment: Assigns strand orientation to additional features such as mutations by orienting them relative to other genomic elements.
• Statistical Analysis: Performs statistical analyses of strand asymmetry patterns.
• Visualization: Generates visualizations of strand asymmetries to facilitate interpretation.

Scientific Applications:

• Transcriptional and Replicative Analysis: Identifies transcriptional and replicative strand asymmetries in germline structural variant breakpoints.
• Transcription Factor Binding Sites: Revealed that 45% of human transcription factor binding sites exhibit significant DNA strand bias within transcribed regions, supported by ChIP-seq analyses.

Methodology:

Takes DNA features with strand annotation as input and outputs analyses of strand asymmetries using statistical analysis and visualization techniques.