This work is part of a project aimed at developing a speech recognition system for language instruction that can assess the quality of pronunciation, identify pronunciation problems, and provide the student with accurate feedback about specific mistakes. Previous work was mainly concerned with scoring the quality of pronunciation. In this work we focus on automatic detection of mispronunciation...

This material may be freely copied for educational purposes, but not for resale, as long as the authors's names and the copyright notice appear clearly on the copies. The authors may be con

The discovery of motifs in DNA sequences remains a fundamental and challenging problem in computational molecular biology and regulatory genomics, although a large number of computational methods have been proposed in the past decade. Among these methods, the Gibbs sampling strategy has shown great promise and is routinely used for finding regulatory motif elements in the promoter regions of co...

A number of computational methods have been proposed for identifying transcription factor binding sites from a set of unaligned sequences that are thought to share the motif in question. We here introduce an algorithm, called cosmo, that allows this search to be supervised by specifying a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may ...

Transcriptional networks are central to any biological process and changes affecting transcription factors or their binding sites in the genome are a key factor driving evolution. As more organisms are being sequenced, tools are needed to easily predict transcription factor binding sites (TFBS) presence and affinity from mere inspection of genomic sequences. Although many TFBS discovery algorit...

Bioluminescent proteins are important for various cellular processes, such as gene expression analysis, drug discovery, bioluminescent imaging, toxicity determination, and DNA sequencing studies. Hence, the correct identification of bioluminescent proteins is of great importance both for helping genome annotation and providing a supplementary role to experimental research to obtain insight into...

MOTIVATION Motif discovery in sequential data is a problem of great interest and with many applications. However, previous methods have been unable to combine exhaustive search with complex motif representations and are each typically only applicable to a certain class of problems. RESULTS Here we present a generic motif discovery algorithm (Gemoda) for sequential data. Gemoda can be applied ...

Many important cellular protein interactions are mediated by peptide recognition domains. The ability to predict a domain's binding specificity directly from its primary sequence is essential to understanding the complexity of protein-protein interaction networks. One such recognition domain is the PDZ domain, functioning in scaffold proteins that facilitate formation of signaling networks. Pre...