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In this paper, we propose a new approach for gene recognition, which uses no training data for the recognizer. In this approach, we start from a simple model, which only uses the knowledge of start codons and the stop codons, then the recognition of the DNA sequences by the recognizer and the training of the parameters of the recognizer by the result of the(More)
The data processing language in a graphical software tool that manages sequence annotation data from genome databases should provide flexible functions for the tasks in molecular biology research. Among currently available languages we adopted the Lua programming language. It fulfills our requirements to perform computational tasks for sequence map layouts,(More)
Single particle analysis is one of the methods for structural studies of protein and macromolecules developed in image analysis on electron microscopy. Reconstructing 3D structure from microscope images is not an easy analysis because of the low resolution of images and lack of the directional information of images in 3D structure. To improve the(More)
In order to clarify the structural changes of the thin filaments related to the regulation mechanism in skeletal muscle contraction, the intensities of thin filament-based reflections in the X-ray fiber diffraction patterns from live frog skeletal muscles at non-filament overlap length were investigated in the relaxed state and upon activation. Modeling the(More)
A new software configuration method using plug-in style components was established for the tool with the incremental development of software used in protein structural study. Our memory database provides the interface of data and functions among plug-in modules and its host program. A molecular structure browser program was developed together with several(More)
We examined the statistical performance of clustering single particle molecular images by bottom-up clustering, a hierarchical algorithm, using simulated protein images with a low signal-to-noise ratio. Using covariance for the measure of similarity together with the iterative alignment, our method was found to be fairly robust against noise. Clustering(More)
We have constructed a general framework for integrating application programs with control through a local Web browser. This method is based on a simple inter-process message function from an external process to application programs. Commands to a target program are prepared in a script file, which is parsed by a message dispatcher program. When it is used(More)
In this article, we describe an improved method to assign the projection angle for averaged images using tilt-pair images for three-dimensional reconstructions from randomly oriented single-particle molecular images. Our study addressed the so-called 'initial volume problem' in the single-particle reconstruction, which involves estimation of projection(More)
To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code(More)