OKseqHMM

OKseqHMM profiles Okazaki fragment sequencing (OK-Seq) data as an R package to measure genome-wide DNA replication fork directionality (RFD) and identify replication initiation and termination zones.

Key Features:

• Replication Fork Directionality Measurement: Directly quantifies RFD from OK-Seq-derived data to characterize replication fork progression.
• Identification of Replication Zones: Calls replication initiation and termination zones, providing insights into the coordination of tens of thousands of DNA replication origins.
• Transcription-Replication Conflict Analysis: Analyzes co-directional and head-on transcription-replication conflicts (TRC) to assess factors affecting genome integrity.
• Hidden Markov Model Algorithm: Applies a Hidden Markov Model (HMM) to segment RFD profiles and improve the accuracy of initiation and termination zone calls.
• Compatibility with Related Techniques: Processes RFD-containing datasets from related methods such as eSPAN and TrAEL-seq in addition to OK-Seq.

Scientific Applications:

• Genome Instability Studies: Mapping replication dynamics to investigate genome instability across diverse cell line models and growth conditions.
• Replication Program and TRC Characterization: Characterizing transcription-replication conflicts and the replication program in yeast, mouse, and human genomes.

Methodology:

Computes RFD from OK-Seq (and compatible eSPAN and TrAEL-seq) datasets from yeast, mouse, and human, applies a Hidden Markov Model to segment RFD profiles and delineate initiation and termination zones, and quantifies co-directional and head-on transcription-replication conflicts.