Background There has been a growing interest in computational discovery of regulatory
elements, and a multitude of motif discovery methods have been proposed. Computational …

Eukaryotic proteins typically contain one or more modular domains such as kinases,
phosphatases, and phoshopeptide-binding domains, as well as characteristic sequence …

We applied an automatic and unsupervised system to a nearly complete database of
mammalian odor receptor genes. The generated motifs and gene classification were …

In the post-genomic era, identification of specific regulatory motifs or transcription factor
binding sites (TFBSs) in non-coding DNA sequences, which is essential to elucidate …

Abstract Motivation: Profile HMMs are a powerful tool for modeling conserved motifs in
proteins. These models are widely used by search tools to classify new protein sequences …

β-barrel membrane proteins are found in the outer membrane of gram-negative bacteria,
mitochondria, and chloroplasts. Although sequence motifs have been studied in α-helical …

In this thesis we have developed novel methods for analyzing biological data, the primary
sequences of the DNA and proteins, the microarray based gene expression data, and other …

Here, we describe a unique probabilistic evaluation of the 20, naturally occurring, amino
acids and their distributions within the Swiss-Prot and Complete Human Genebank …

Motifs are overrepresented sequence or spatial patterns appearing in proteins. They often
play important roles in maintaining protein stability and in facilitating protein function. When …

Motivation: Multiple sequence alignment at the level of whole proteomes requires a high
degree of automation, precluding the use of traditional validation methods such as manual …