A Unified Approach for Reconstructing Ancient Gene Clusters
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Finding Nested Common Intervals Efficiently
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
The incompatible desiderata of gene cluster properties
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Integer linear programs for discovering approximate gene clusters
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Tractability results for the consecutive-ones property with multiplicity
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
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In comparative genomics, various combinatorial models can be used to specify gene clusters--groups of genes that are co-located in a set of genomes. Several approaches have been proposed to reconstruct putative ancestral gene clusters based on the gene order of contemporary species. One prevalent and natural reconstruction criterion is consistency: For a set of reconstructed gene clusters, there should exist a gene order that comprises all given clusters. In this paper, we discuss the consistency problem for different gene cluster models on sequences with restricted gene multiplicities. Our results range from linear-time algorithms for the simple model of adjacencies to NP completeness for more complex models like common intervals.