Showing papers by "Costas S. Iliopoulos published in 2021"
01 Aug 2021
TL;DR: This article presents an algorithm for solving the pattern matching problem with a solid pattern and an elastic-degenerate text running in \(\mathcal {O}(N+\alpha \gamma mn)\) time; where m is the length of the pattern; n and N are the length and total size of the elastic-degreeate text, respectively.
Abstract: Motivated by applications in bioinformatics, in what follows, we extend the notion of gapped strings to elastic-degenerate strings An elastic-degenerate string can been seen as an ordered collection of solid (standard) strings interleaved by elastic-degenerate symbols; each such symbol corresponds to a set of two or more variable-length solid strings In this article, we present an algorithm for solving the pattern matching problem with a solid pattern and an elastic-degenerate text running in \(\mathcal {O}(N+\alpha \gamma mn)\) time; where m is the length of the pattern; n and N are the length and total size of the elastic-degenerate text, respectively; \(\alpha \) and \(\gamma \) are parameters, respectively representing the maximum number of strings in any elastic-degenerate symbol of the text and the maximum number of elastic-degenerate symbols spanned by any occurrence of the pattern in the text The space used by the proposed algorithm is \(\mathcal {O}(N)\)
27 citations
18 Apr 2021
TL;DR: In this paper, the problem of computing the shortest cover of a cyclic shift of a string of length n has been studied, and it has been shown that the number of different lengths of shortest covers of cyclic shifts of the same string can be computed in polynomial time.
Abstract: A factor W of a string X is called a cover of X, if X can be constructed by concatenations and superpositions of W. Breslauer (IPL, 1992) proposed a well-known \(\mathcal {O}(n)\)-time algorithm that computes the shortest cover of every prefix of a string of length n. We show an \(\mathcal {O}(n \log n)\)-time algorithm that computes the shortest cover of every cyclic shift of a string and an \(\mathcal {O}(n)\)-time algorithm that computes the shortest among these covers. A related problem is the number of different lengths of shortest covers of cyclic shifts of the same string of length n. We show that this number is \(\varOmega (\log n)\).
3 citations
TL;DR: IUPACpal as discussed by the authors is a tool for identifying inverted repeat in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats, and it has been shown that it can identify many previously unidentified inverted repeat when compared with EMBOSS, and also performed with orders of magnitude improved speed.
Abstract: An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions. Many international consortia provide a comprehensive description of common genetic variation making alternative sequence representations, such as IUPAC encoding, necessary for leveraging the full potential of such broad variation datasets. We present IUPACpal, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats. Within the parameters that were tested, our experimental results show that IUPACpal compares favourably to a similar application packaged with EMBOSS. We show that IUPACpal identifies many previously unidentified inverted repeats when compared with EMBOSS, and that this is also performed with orders of magnitude improved speed.