The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

/pdf/clustal-w-improving-the-sensitivity-of-progressive-multiple-2na2s9sq2h.pdf

Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces),the server circumvents the problem of portability of this software. Detailed output,in the form of structure plots with or without reliability information,single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information,but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/ mfold. This URL will be referred to as ‘MFOLDROOT’.

/pdf/mfold-web-server-for-nucleic-acid-folding-and-hybridization-3pzoe1h05m.pdf

Mfold web server for nucleic acid folding and hybridization prediction

https://njc.rockefeller.edu/pdf4/Class2-LeeAmbros1993.pdf

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Subpopulations of RNA molecules that bind specifically to a variety of organic dyes have been isolated from a population of random sequence RNA molecules. Roughly one in 10(10) random sequence RNA molecules folds in such a way as to create a specific binding site for small ligands.

In vitro selection of RNA molecules that bind specific ligands.

The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system. The programs available and the conditions for transfer are described.

/pdf/a-comprehensive-set-of-sequence-analysis-programs-for-the-luj6w12mfm.pdf

A comprehensive set of sequence analysis programs for the VAX

Computer graphics research has concentrated on creating photo-realistic images of synthetic objects. These images communicate surface shading and curvature, as well as the depth relationships of objects in a scene. These renderings are traditionally represented by a rectangular array of pixels that tile the image plane.As an alternative to photo-realism, it is possible to create abstract images using an ordered collection of brush strokes. These abstract images filter and refine visual information before it is presented to the viewer. By controlling the color, shape, size, and orientation of individual brush strokes, impressionistic paintings of computer generated or photographic images can easily be created.

/pdf/paint-by-numbers-abstract-image-representations-xb0mftd986.pdf

Paint by numbers: abstract image representations

Generating images of texture mapped geometry requires projecting surfaces onto a two-dimensional screen. If this projection involves perspective, then a division must be performed at each pixel of the projected surface in order to correctly calculate texture map coordinates. We show how a simple extension to perspective-comect texture mapping can be used to create various lighting effects, These in- clude arbitrary projection of two-dimensional images onto geom- etry, realistic spotlights, and generation of shadows using shadow maps( 10). These effects are obtained in real time using hardware that performs correct texture mapping.

/pdf/fast-shadows-and-lighting-effects-using-texture-mapping-2vb6d10s30.pdf

Fast shadows and lighting effects using texture mapping

This paper describes a system architecture that supports realtime generation of complex images, efficient generation of extremely high-quality images, and a smooth trade-off between the two.Based on the paradigm of integration, the architecture extends a state-of-the-art rendering system with an additional high-precision image buffer. This additional buffer, called the Accumulation Buffer, is used to integrate images that are rendered into the framebuffer. While originally conceived as a solution to the problem of aliasing, the Accumulation Buffer provides a general solution to the problems of motion blur and depth-of-field as well.Because the architecture is a direct extension of current workstation rendering technology, we begin by discussing the performance and quality characteristics of that technology. The problem of spatial aliasing is then discussed, and the Accumulation Buffer is shown to be a desirable solution. Finally the generality of the Accumulation Buffer is explored, concentrating on its application to the problems of motion blur, depth-of-field, and soft shadows.

/pdf/the-accumulation-buffer-hardware-support-for-high-quality-450nv0mgog.pdf

The accumulation buffer: hardware support for high-quality rendering

This paper describes a 3D object-space paint program. This program allows the user to directly manipulate the parameters used to shade the surface of the 3D shape by applying pigment to its surface. The pigment has all the properties normally associated with material shading models. This includes, but is not limited to, the diffuse color, the specular color, and the surface roughness. The pigment also can have thickness, which is modeled by simultaneously creating a bump map attached to the shape. The output of the paint program is a 3D model with associated texture maps. This information can be used with any rendering program with texture mapping capabilities. Almost all traditional techniques of 2D computer image painting have analogues in 3D object painting, but there are also many new techniques unique to 3D. One example is the use of solid textures to pattern the surface.

Direct WYSIWYG painting and texturing on 3D shapes: (An error occurred during the printing of this article that reversed the print order of pages 118 and 119. While we have corrected the sort order of the 2 pages in the DL, the PDF did not allow us to repaginate the 2 pages.)

Paul Haeberli

Papers

A comprehensive set of sequence analysis programs for the VAX

Paint by numbers: abstract image representations

Fast shadows and lighting effects using texture mapping

The accumulation buffer: hardware support for high-quality rendering

Direct WYSIWYG painting and texturing on 3D shapes: (An error occurred during the printing of this article that reversed the print order of pages 118 and 119. While we have corrected the sort order of the 2 pages in the DL, the PDF did not allow us to repaginate the 2 pages.)