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Article
Open AccessCable bacteria with electric connection to oxygen attract flocks of diverse bacteria
Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This act...
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Protocol
polyDFE: Inferring the Distribution of Fitness Effects and Properties of Beneficial Mutations from Polymorphism Data
The possible evolutionary trajectories a population can follow is determined by the fitness effects of new mutations. Their relative frequencies are best specified through a distribution of fitness effects (DF...
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Article
Open AccessRegmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments
Motif analysis methods have long been central for studying biological function of nucleotide sequences. Functional genomics experiments extend their potential. They typically generate sequence lists ranked by ...
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Article
Open AccessEvolving stochastic context-free grammars for RNA secondary structure prediction
Stochastic Context–Free Grammars (SCFGs) were applied successfully to RNA secondary structure prediction in the early 90s, and used in combination with comparative methods in the late 90s. The set of SCFGs pot...
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Article
Open AccessComparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains
Continuous time Markov chains (CTMCs) is a widely used model for describing the evolution of DNA sequences on the nucleotide, amino acid or codon level. The sufficient statistics for CTMCs are the time spent i...
