Genome Rearrangements with Partially Ordered Chromosomes
Genomic maps often do not specify the order within some groups of two or more markers. The synthesis of a master map from several sources introduces additional order ambiguity due to markers missing from some sources. We represent each chromosome as a partial order, summarized by a directed acyclic graph (DAG), to account for poor resolution and of missing data. The genome rearrangement problem is then to infer a minimum number of translocations and reversals for transforming a set of linearizations, one for each chromosomal DAG in the genome of one species, to linearizations of the DAGs of another species. We augment each DAG to a directed graph (DG)in which all possible linearizations are embedded. The chromosomal DGs representing two genomes are combined to produce a single bicoloured graph. ProM this we extract a maximal decomposition into alternating coloured cycles, determining an optimal sequence of rearrangements. We test this approach on simulated partially ordered genomes.
Chunfang Zheng David Sankoff
Department of Biology University of Ottawa, Canada KIN 6N5 Department of Mathematics and Statistics University of Ottawa, Canada KIN 6N5
国际会议
The 11th Annual International Computing and Combinatorics Conference COCOON 2005(第11届国际计算和组合会议)
昆明
英文
52-62
2005-08-01（万方平台首次上网日期，不代表论文的发表时间）