WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Tests for Gene Clusters Satisfying the Generalized Adjacency Criterion
BSB '08 Proceedings of the 3rd Brazilian symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The incompatible desiderata of gene cluster properties
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
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Given the gene orders in two modern genomes, it may be difficult to decide if some genes are close enough in both genomes to infer some ancestral proximity or some functional relationship. Current methods all depend on arbitrary parameters. We explore a two-parameter class of gene proximity criteria, and find natural values for these parameters. One has to do with the parameter value where the expected information contained in two genomes about each other is maximized. The other has to do with parameter values beyond which all genes are clustered. We analyse these using combinatorial and probabilistic arguments as well as simulations.