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Retroviruses are believed to been important in the evolution of genome organization in biological organisms. This study investigates the impact of virtual retroviruses on the genome organization of an artificial organism using the simulation environment developed in. The artificial organisms, grid walkers, were designed to be a model of biological organisms. They have a complex fitness landscape with...
Side effect machines operate by associating side effects with the states of a finite state machine. The use of side effect machines permits the researcher to leverage information stored in the state transition structure, making machines that might be identical as recognizers behave differently as classifiers. The side effect machines in this study associate a counter with each state so that the number...
This study presents a strategy for reducing the effects of noise on the location of RNA motifs in the context of a previously developed analysis pipeline. The pipeline was developed to search for novel RNA motifs incorporating both primary and secondary structure. The ability of the pipeline to detect motifs in the presence of a relatively large amount of sequence not containing a target motif is...
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