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Cytosine methylation is a DNA modification that has great impact on the regulation of gene expression and important implications for the biology and health of several living beings, including humans. Bisulfite conversion followed by next generation sequencing (BS-seq) of DNA is the gold standard technique used to detect DNA methylation at single-base(More)
In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these measures. We describe two data structures whose size depends on multiple measures of repetition at once, and that provide(More)
The high throughput of modern NGS sequencers coupled with the huge sizes of genomes currently analysed, poses always higher algorithmic challenges to align short reads quickly and accurately against a reference sequence. A crucial, additional, requirement is that the data structures used should be light. The available modern solutions usually are a(More)
We consider the problem of indexing a text T (of length n) with a light data structure that supports efficient search of patterns P (of length m) allowing errors under the Hamming distance. We propose a hash-based strategy that employs two classes of hash functions—dubbed Hamming-aware and de Bruijn—to drastically reduce search space and memory footprint of(More)
Bisulfite treatment of DNA followed by sequencing (BS-seq) has become a standard technique in epigenetic studies, providing researchers with tools for generating single-base resolution maps of whole methylomes. Aligning bisulfite-treated reads, however, is a computationally difficult task: bisulfite treatment decreases the (lexical) complexity of(More)
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for locating all the exact occurrences of a pattern in a highly-repetitive string take advantage of a single measure of(More)
We consider the problem of building a compressed fully-indexable dictionary over a set S of n items out of a universe U = {0, ..., u − 1}. We use gap-encoding combined with entropy compression in order to reduce the space of our structures. Let H gap 0 be the zero-order empirical entropy of the gap stream. We observe that nH gap 0 ∈ o(gap) if the gaps are(More)