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Multiple alignment by aligning alignments
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The effect of sequence quality on sequence alignment
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A structural alignment kernel for protein structures
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Combining statistical alignment and phylogenetic footprinting to detect regulatory elements
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Rahul Satija, Lior Pachter, Jotun Hein
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RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
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Xing Xu, Yongmei Ji, Gary D. Stormo
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Comparative modeling without implicit sequence alignments
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Andrzej Kolinski, Dominik Gront
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