Reconstructing evolutionary history of human gene clusters

CREATED: 200803300355 Gene clusters = clusters of genes generated by segmental duplication

** Motivation

• significant challenge to genome sequencing
• represents area of functionary innovation ** Problem
• Given a DNA sequence, recover sequence of duplication, deletion events
• Basic algorithm: find a duplication event and remove it repeatedly ** Probabilistic extension
• handle model violations, noise, missing data and incoporate evolutionary models
• Build evolutionary events to a probabilistic model, deletions and alignment boundaries are treated as random events
• Using importance sampling to reconstruct the history
• Make inference via weighted average from multiple reconstructed histories ** Results
• PRAME gene cluster
• use BlastZ to find alignment and construct dot-plot