WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Improved approximate common interval
Information Processing Letters
More efficient algorithms for closest string and substring problems
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Integer linear programs for discovering approximate gene clusters
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Faster query algorithms for the text fingerprinting problem
Information and Computation
Output-Sensitive Algorithms for Finding the Nested Common Intervals of Two General Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Whole genome comparison based on the analysis of gene cluster conservation has become a popular approach in comparative genomics. While gene order and gene content as a whole randomize over time, it is observed that certain groups of genes which are often functionally related remain co-located across species. However, the conservation is usually not perfect which turns the identification of these structures, often referred to as approximate gene clusters, into a challenging task. In this paper, we present a polynomial time algorithm that computes approximate gene clusters based on reference occurrences. We show that our approach yields highly comparable results to a more general approach and allows for approximate gene cluster detection in parameter ranges currently not feasible for non-reference based approaches.