We present two variations of Duval’s algorithm for computing the Lyndon factorization of a word. The first algorithm is designed for the case of small alphabets and is able to skip a significant portion of the characters of the string, for strings containing runs of the smallest character in the alphabet. Experimental results show that it is faster than Duval’s original algorithm, more than ten...

We introduce a Partial Order Kernel (POKer) on the weighted sum of local alignment scores that can be used for comparison and classification of strings containing alternative substrings of variable length. POKer is defined over the product of two directed acyclic graphs, each representing a string with alternative substrings, and is computed efficiently using dynamic programming. We evaluate th...

Watson-Crick D0L systems, introduced in 1997 by V. Mihalache and A. Salomaa, arise from two major principles: the Lindenmayer rewriting and the Watson-Crick complementarity principle. Complementarity can be viewed as a purely language-theoretic operation. Majority of a certain type of symbols in a string (purines vs. pyrimidines) triggers a transition to the complementary string. The paper deal...

This paper presents our approach to the 2013 Native Language Identification shared task, which is based on machine learning methods that work at the character level. More precisely, we used several string kernels and a kernel based on Local Rank Distance (LRD). Actually, our best system was a kernel combination of string kernel and LRD. While string kernels have been used before in text analysi...

Exact string Searching is one of the most important problems that had been investigated by many studies ranging from finding the shortest common super string in DNA sequencing to searching for occurrences of a pattern occurs in text editors. In this paper, a new Enhanced Checking and Skipping Algorithm (ECSA) is introduced. The new algorithm enhance the classical string searching algorithms by ...

The formation of DNA-based nanostructures involves the binding of different kinds of ligands to DNA as well as the interaction of DNA molecules with each other. Complex formation between ligand and DNA can alter physicochemical properties of the DNA molecule. In the present work, the accessibility of DNAligand complexes to cleavage by DNase I are considered, and the exact algorithms for analysi...

Strings and sequences are ubiquitous in many areas of data analysis. However, only few learning methods can be directly applied to this form of data. We present Sally, a tool for embedding strings in vector spaces that allows for applying a wide range of learning methods to string data. Sally implements a generalized form of the bag-of-words model, where strings are mapped to a vector space tha...