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We present a self-adjusting layout scheme for suffix trees in secondary storage that provides optimal number of disk accesses for a sequence of string or substring queries. This has been an open problem since Sleator and Tarjan presented their splaying technique to create self-adjusting binary search trees in 1985. In addition to resolving this open(More)
We developed a novel Designed Primer-based RNA-sequencing strategy (DP-seq) that uses a defined set of heptamer primers to amplify the majority of expressed transcripts from limiting amounts of mRNA, while preserving their relative abundance. Our strategy reproducibly yielded high levels of amplification from as low as 50 picograms of mRNA while offering a(More)
DNA-protein alignment algorithms can be used to discover coding sequences in a genomic sequence, if the corresponding protein derivatives are known. They can also be used to identify potential coding sequences of a newly sequenced genome, by using proteins from related species. Previously known algorithms either solve a simplified formulation, or sacrifice(More)
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