Computational geometry: an introduction
Computational geometry: an introduction
Art gallery theorems and algorithms
Art gallery theorems and algorithms
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
On Suboptimal Alignments of Biological Sequences
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
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The DNA sequence assembler we built for the whole genome shotgun assembly of the human genome, utilizes end-reads of inserts to order and orient assembled contigs into scaffolds for which the distances between consecutive contigs are statistically characterized. We consider the problem of comparing two such scaffolds. Applications include comparison of two distinct assemblies for mutual confirmation, and comparison of scaffold assemblies of BACs to determine a whole genome tiling of the BACs. We formalize the problem and develop efficient algorithms for a number of variations of the problem, the essential result being a sparse algorithm that refines gap estimates based on the overlap evidence.