Journal
JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 17, Issue 11, Pages 1561-1573Publisher
MARY ANN LIEBERT, INC
DOI: 10.1089/cmb.2009.0268
Keywords
breakpoint distance; comparative genomics; consensus genetic map; integer linear programming
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Funding
- Singapore NRF [NRF2007IDM-IDM002-010]
- MOE AcRF [RG78/08]
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The construction of consensus genetic maps is a very challenging problem in computational biology. Many computational approaches have been proposed on the basis of only the marker order relations provided by a given set of individual genetic maps. In this article, we propose a comparative approach to constructing consensus genetic maps for a genome, which further takes into account the order relations from a closely related genome when resolving ordering conflicts among individual genetic maps. It aims to retain as many order relations as possible from individual genetic maps while achieving the minimum rearrangement distance to the reference genome. We implement the proposed approach as an integer linear program and test it on both simulated and real biological datasets. The experimental results show that it is capable of constructing more accurate consensus genetic maps than the most recent approach called MERGEMAP.
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