Motivation: Motif detection for DNA sequences has many important applications in biological studies, e.g., locating binding sites and regulatory signals, and designing genetic prob...
Markov order-1 conditional random fields (CRFs) and semi-Markov CRFs are two popular models for sequence segmentation and labeling. Both models have advantages in terms of the typ...
In this paper we investigate the general problem of discovering recurrent patterns that are embedded in categorical sequences. An important real-world problem of this nature is mo...
Understanding the mechanismsthat determine the regulation of geneexpression is an important and challenging problem. A fundamental subproblem is to identify DNA-bindingsites for u...
: Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)space and almost always runs in O(k.n)-...