منابع مشابه
Hardness of Optimal Spaced Seed Design
Speeding up approximate pattern matching is a line of research in stringology since the 80’s. Practically fast approaches belong to the class of filtration algorithms, in which text regions dissimilar to the pattern are excluded (filtered out) in a first step, and remaining regions are compared to the pattern by dynamic programming in a second step. Among the necessary conditions used to test s...
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Optimal spaced seeds were developed as a method to increase sensitivity of local alignment programs similar to BLASTN. Such seeds have been used before in the program PatternHunter, and have given improved sensitivity and running time relative to BLASTN in genome-genome comparison. We study the problem of computing optimal spaced seeds for detecting homologous coding regions in unannotated geno...
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Spaced seed is a filter method invented to efficiently identify the regions of interest in similarity searches. It is now well known that certain spaced seeds hit (detect) a randomly sampled similarity region with higher probabilities than the others. Assume each position of the similarity region is identity with probability p independently. The seed optimization problem seeks for the optimal s...
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De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features fo...
متن کاملHardness of robust network design
The authors settle the complexity status of the robust network design problem in undirected graphs. The fact that the flow-cut gap in general graphs can be large, poses some difficulty in establishing a hardness result. Instead, the authors introduce a single-source version of the problem where the flow-cut gap is known to be one. They then show that this restricted problem is coNP-Hard. This v...
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ژورنال
عنوان ژورنال: Journal of Computer and System Sciences
سال: 2008
ISSN: 0022-0000
DOI: 10.1016/j.jcss.2007.10.001