PT  - JOURNAL ARTICLE
AU  - Paolo Ferragina
AU  - Bud Mishra
TI  - Algorithms in Stringomics (I): Pattern-Matching against “Stringomes”
AID  - 10.1101/001669
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 001669
4099  - http://biorxiv.org/content/early/2014/01/02/001669.short
4100  - http://biorxiv.org/content/early/2014/01/02/001669.full
AB  - 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.