This paper develops an evolutionary method that learns inductively to recognize the makeup and the position of very short consensus sequences, which are a typical feature of promoters in eukaryotic genomes. This class of method can be used to discover candidate promoter sequences in primary sequence data. If further developed, it has the potential to discover genes which are regulated together.

In this article, we address the problem of modeling generic features of structurally but not textually related DNA motifs, that is, motifs whose consensus sequences are entirely different but nevertheless share "metasequence features" reflecting similarities in the DNA-binding domains of their associated protein recognizers. We present MotifPrototyper, a profile Bayesian model that can capture ...

RNA structural motifs are recurrent structural elements occurring in RNA molecules. They play essential roles in consolidating RNA tertiary structures and in binding proteins. Recently, we identified a new type of RNA structural motif, namely λ-turn, from ribosomal RNAs. This motif has a helix-internal loop-helix structure. The directions of its two helices are changed *90° due to the existence...

MOTIVATION A typical PSI-BLAST search consists of iterative scanning and alignment of a large sequence database during which a scoring profile is progressively built and refined. Such a profile can also be stored and used to search against a different database of sequences. Using it to search against a database of consensus rather than native sequences is a simple add-on that boosts performance...

objective(s): production of a recombinant and immunogenic antigen using dengue virus type-3 envelope protein is a key point in dengue vaccine development and diagnostic researches. the goals of this study were providing a recombinant protein from dengue virus type-3 envelope protein and evaluation of its immunogenicity in mice. materials and methods: multiple amino acid sequences of different i...

A three dimensional model of the basic Helix-Loop-Helix motif and its sequence specific recognition of DNA is described. The basic-helix I is modeled as a continuous ?-helix because no ?-helix breaking residue is found between the basic region and the first helix. When the basic region of the two peptide monomers are aligned in the successive major groove of the cognate DNA, the hydrophobi...

Esox lucius is an economically important freshwater species. Mitochondrial cytb, 12SrRNA, and 16SrRNA gene sequences were used in order to clarify the genetic variation and population structure in three E. Lucius populations, i.e., one Wild population (W) and two hatchery populations (Hatchery Population I-HPI and Hatchery Population II-HPII). A total of 55 individuals, with 19 from wild and 1...