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PANDAseq: paired-end assembler for illumina sequences
TLDR
ConclusionsPANDAseq rapidly assembles sequences and scales to billions of paired-end reads with the correction of most errors. Expand
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Integer programming approaches to haplotype inference by pure parsimony
TLDR
In 2003, Gusfield introduced the haplotype inference by pure parsimony (HIPP) problem and presented an integer program (IP) that quickly solved many simulated instances of the problem. Expand
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Predicting vegetation types at treeline using topography and biophysical disturbance variables
. The relationships between four vegetation types and variables representing topography and biophysical disturbance gradients were modeled for a study area in east-central Glacier National Park,Expand
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A New Integer Programming Formulation for the Pure Parsimony Problem in Haplotype Analysis
TLDR
We present a new integer programming formulation for the haplotype inference by pure parsimony (HIPP) problem that can solve substantially larger problems than are practical with Gusfield’s formulation, though it is is much slower. Expand
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Vector seeds: An extension to spaced seeds
TLDR
We present improved techniques for finding homologous regions in DNA and protein sequences that allow marked improvements in both specificity and sensitivity. Expand
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Integer Programming Formulations and Computations Solving Phylogenetic and Population Genetic Problems with Missing or Genotypic Data
TLDR
We describe a set of related integer linear programming (ILP) formulations for several additional combinatorial problems, most of which are known to be NP-hard. Expand
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ExonHunter: a comprehensive approach to gene finding
TLDR
We present ExonHunter, a new and comprehensive gene finder based on a hidden Markov model that outperforms existing systems and features several new ideas and approaches. Expand
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Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions
TLDR
We study the problem of computing optimal spaced seeds for detecting sequences generated by a Hidden Markov model, and show that the optimal seeds are substantially more sensitive than the seeds used in the standard alignment program BLAST, and also substantially better than those of PatternHunter. Expand
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The combined effect of incubation temperature, pH and sorbic acid on the probability of growth of non-proteolytic, type B Clostridium botulinum.
It has been reported that non-proteolytic strains of Clostridium botulinum will grow at 3.3 degrees C, and they are therefore of concern in relation to certain chilled foods. The effects ofExpand
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Optimal Spaced Seeds for Homologous Coding Regions
TLDR
We study the problem of computing optimal spaced seeds for detecting homologous coding regions in unannotated genomic sequences. Expand
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