Ritu Kundu

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A degenerate symbol x̃ over an alphabet Σ is a non-empty subset of Σ, and a sequence of such symbols is a degenerate string. A degenerate string is said to be conservative if its number of non-solid symbols is upper-bounded by a fixed positive constant k. We consider here the matching problem of conservative degenerate strings and present the first(More)
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual’s genome in order to catalogue sequence variation and understand its biological consequences. Wholegenome sequencing techniques currently produce masses of data in the form of short sequences known as reads. Assembling these reads into a whole genome(More)
Longest common extension queries (LCE queries) and runs are ubiquitous in algorithmic stringology. Linear-time algorithms computing runs and preprocessing for constant-time LCE queries have been known for over a decade. However, these algorithms assume a linearly-sortable integer alphabet. A recent breakthrough paper by Bannai et. al. (SODA 2015) showed a(More)
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such that each elastic-degenerate symbol corresponds to a set of two or more variable length strings. Here, we present an(More)