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We present a novel method for prediction of common structures and alignment for two homologous RNA sequences. The method, termed joint sampling, is based on sampling from the structural alignment space of the sequences, i.e. the space of joint representations of common secondary structures and sequence alignments of the sequences. The structural alignment space is efficiently sampled by probabilistically...
We propose an algorithm for estimating the common secondary structure, alignment, and posterior base pairing probabilities for two RNA sequences. A definition of structural alignment is presented based on a novel concept of matched helical regions that generalizes the common secondary structure and alignment constraints used in prior work. A probabilistic framework for scoring structural alignments...
Prediction of common secondary structure across multiple RNA sequences is known to significantly increase accuracy in comparison with single-sequence based prediction methods. However, the computational requirements for joint prediction can often be daunting in comparison to single-sequence prediction. As a result, heuristic simplifications are often necessary for this joint estimation problem in...
A focal plane detector system has been developed for the Rochester Recoil Mass Spectrometer. It consists of a parallel grid avalanche counter (PGAC) backed by an ionization counter (IC). The PGAC is used to obtain the horizontal and vertical position of the incident particles and also to provide a fast timing signal. The PGAC has an active area of 5.1 cm 5.1 cm. The IC consists of three charge...
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