Efficient algorithms for analyzing segmental duplications  with deletions and inversions in genomes.
BACKGROUND
Segmental duplications, or low-copy repeats, are common in mammalian genomes.  In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organization complicates analysis of the evolutionary history of these sequences.   One model proposed to explain this mosaic patterns is a model of repeated aggregation and subsequent duplication of genomic sequences.


RESULTS
We describe a polynomial-time exact algorithm to compute duplication distance, a genomic distance defined as the most parsimonious way to build a target string by repeatedly copying substrings of a fixed source string.  This distance models the process of repeated aggregation and duplication.   We also describe extensions of this distance to include certain types of substring deletions and inversions.  Finally, we provide a description of a sequence of duplication events as a context-free grammar (CFG).


CONCLUSIONS
These new genomic distances will permit more biologically realistic analyses of segmental duplications in genomes.
Kahn
Crystal L
CL
Mozes
Shay
S
Raphael
Benjamin J
BJ