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bioRxiv · 10.1101/001669

Algorithms in Stringomics (I): Pattern-Matching against "Stringomes"

Paolo Ferragina·Bud (Bhubaneswar) Mishra
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Abstract

This paper reports an initial design of new data-structures that generalizes the idea of pattern-matching in stringology, from its traditional usage in an (unstructured) set of strings to the arena of a well-structured family of strings. In particular, the object of interest is a family of strings composed of blocks/classes of highly similar \"stringlets,\" and thus mimic a population of genomes made by concatenating haplotype-blocks, further constrained by haplotype-phasing. Such a family of strings, which we dub \"stringomes,\" is formalized in terms of a multi-partite directed acyclic graph with a source and a sink. The most interesting property of stringomes is probably the fact that they can be represented efficiently with compression up to their k-th order empirical entropy, while ensuring that the compression does not hinder the pattern-matching counting and reporting queries - either internal to a block or spanning two (or a few constant) adjacent blocks. The solutions proposed here have immediate applications to next-generation sequencing technologies, base-calling, expression profiling, variant-calling, population studies, onco-genomics, cyber security trace analysis and text retrieval.

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Paolo Ferragina, Bud (Bhubaneswar) Mishra. 2014-01-02. Algorithms in Stringomics (I): Pattern-Matching against "Stringomes". https://doi.org/10.1101/001669

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