David Sankoff

Title: Removing Noise and Ambiguities from Comparative Maps in Rearrangement

Analysis


Comparison of genetic maps is hampered by errors and ambiguities
introduced by mapping technology, unresolved paralogy and genome
rearrangement.  We present an analysis for resolving these problems
and extracting corrected data so that markers occur in consecutive
strips in both genomes.  To this end, we introduce the notion of pre-
strip, an efficient way of generating these,  and  a compatibility
analysis culminating in a Maximum Weighted Clique search.  The output
can be directly analyzed with genome rearrangement algorithms.  We
investigate the trade-off between the retention of as many markers as
possible in the solution versus the production of a plausible
rearrangement analysis.   We explore these questions through
simulation and through comparison of the rice and sorghum genomes.

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