Set of novel tools for PCR primer design.

We have developed a new package of computer programs and algorithms for different PCR applications, including allele-specific PCR, multiplex PCR, and long PCR. The package is included in the upcoming VectorNTI suite software and attempts to incorporate most of the current knowledge about PCR primer design. A wide range of primer characteristics is available for user manipulation to provide improved efficiency and increased flexibility of primer design. To accelerate the primer calculations, we have optimized algorithms using recent advances in computer science such as dynamic trees and lazy evaluation. Proper structural organization of input parameters provides further program acceleration. New Vector NTI primer design software allows calculations of primer pairs for long PCR amplification of 120-kb genomic DNA in 5 min under most stringent input parameters and clustering 435 primer pairs for multiplex PCR within 30 min on a standard Pentium III PC. Our program allows the user to take advantage of molecule annotation by applying different kinds of filtering features during PCR primer design.     

Crystallographic protein model-building on the web

X-ray crystallography is the most widely used method to determine the 3D structure of protein molecules. One of the most difficult steps in protein crystallography is model-building, which consists of constructing a backbone and then amino acid side chains into an electron density map. Interpretation of electron density maps represents a major bottleneck in protein structure determination pipelines, and thus, automated techniques to interpret maps can greatly improve the throughput. We have developed WebTex, a simple and yet powerful web interface to TEXTAL, a program that automates this process of fitting atoms into electron density maps. TEXTAL can also be downloaded for local installation. Availability: Web interface, downloadable binaries and documentation at http://textal.tamu.edu     

Using computational grid capabilities to enhance the capability of an X‐ray source for structural biology

The Advanced Photon Source at Argonne National Laboratory enables structural biologists to perform state-of-the-art crystallography diffraction experiments with high-intensity X-rays. The data gathered during such experiments is used to determine the molecular structure of macromolecules to enhance, for example, the capabilities of modern drug design for basic and applied research. The steps involved in obtaining a complete structure are computationally intensive and require the proper adjustment of a considerable number of parameters that are not known a priori. Thus, it is advantageous to develop a computational infrastructure for solving the numerically complex problems quickly, in order to enable quasi-real-time information discovery and computational steering. Specifically, we propose that the time-consuming calculations be performed in a “computational grid” accessing a large number of state-of-the-art computational facilities. Furthermore, we envision that experiments could be conducted by researchers at their home institution via remote steering while a beamline technician performs the actual experiment; such an approach would be cost-efficient for the user. We conducted a case study involving multiple tasks of a structural biologist, including data acquisition, data reduction, solution of the phase problem, and calculation of the final result - an electron density map, which is subsequently used for modeling of the molecular structure. We developed a parallel program for the data reduction phase that reduces the turnaround time significantly. We also distributed the solution of the phase problem in order to obtain the resulting electron density map more quickly. We used the GUSTO testbed provided by the Globus metacomputing project as the source of the necessary state-of-the-art computational resources, including workstation clusters. This revised version was published online in July 2006 with corrections to the Cover Date.     

New programs: XELE—a polypeptide model-building program for a graphics workstation

A model-building program, XELE, for use in protein crystallography has been written in C under UNIX on a graphics workstation. This program makes full use of the X Window system to display the electron density distribution and to manipulate the polypeptide model, and therefore is named XELE. It utilizes a fast three-dimensional rendering package, Dorè, and is portable to other types of graphics workstations. A part of the program for the man-machine interface uses the library of X Window and X Toolkit, and therefore is highly interactive. The structure analysis program package, PROTEIN, is also implemented in an interactive mode using X Window, and has been interfaced with XELE.     

A visual data flow environment for macromolecular crystallographic computing

This article describes the integration of programs from the widely used CCP4 macromolecular crystallography package into a modern data flow visualization environment (application visualization system [AVS]), which provides a simple graphical user interface, a visual programming paradigm, and a variety of 1-, 2-, and 3-D data visualization tools for the display of graphical information and the results of crystallographic calculations, such as electron density and Patterson maps. The CCP4 suite comprises a number of separate Fortran 77 programs, which communicate via common file formats. Each program is encapsulated into an AVS macro module, and may be linked to others in a data flow network, reflecting the nature of many crystallo-graphic calculations. Named pipes are used to pass input parameters from a graphical user interface to the program module, and also to intercept line printer output, which can be filtered to extract graphical information and significant numerical parameters. These may be passed to downstream modules, permitting calculations to be automated if no user interaction is required, or giving the user the opportunity to make selections in an interactive manner.     

Crystal structure of a lysozyme-tetrasaccharide lactone complex

The binding of a proposed transition-state analogue, the δ-lactone derived from tetra-N-acetylchitotetraose, to lysozyme in the crystal at pH 2.6 has been studied by X-ray diffraction techniques to a resolution of 2.5 Å. The tetrasaccharide lactone is bound in sites A, B, C, D with sugar residues located in sites A, B and C in similar positions to those observed previously in the complex with tri-N-acetylchitotriose. Analysis of the electron density map for site D, by direct model-building and with a computer model-building programme, indicates that the δ-lactone ring is in a conformation close to a sofa or a boat which brings the hydroxymethyl group C₍₆₎O₍₆₎ axial. These studies provide support for the role of strain in the proposed mechanism of lysozyme catalysis. The orientation of the lactone group in site D is slightly different from that originally derived by hypothetical model-building.     

Calculation of hydrodynamic properties of globular proteins from their atomic-level structure

The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program.     

Markov random field based automatic image alignment for electron tomography

We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.     

genalex 6: genetic analysis in Excel. Population genetic software for teaching and research

genalex is a user‐friendly cross‐platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency‐based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance‐based calculations include amova , principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and twogener . More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, genalex 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/     

Computer video acquisition and analysis system for biological data

The BIAS (Biological Image Analysis System) was developed to:(i) permit accurate entry and image processing of biologicaldata; (ii) minimize the need for specialized hardware; and (iii)aid in the human genome mapping and other projects. The firstmouse/cursor key-driven module was designed to be user interactiveand readily accessible to many laboratories. It contains theDRSNDS programs which automate the entering of data in a systematicformat. The types of data that can be entered utilizing thismodule are DNA — RNA gels from either a positive or negativePolaroid^TM image, autoradiograms or biotinylated images fromSouthern, Northern and dot or slot blot hybridization analyses.The image is acquired using a video camera and then digitizedfor subsequent analysis. During the analysis graphical representationsof the intermediate results are provided to assure user confidence.At any point within the program the user may obtain on-linehelp with the current task. The output displays the mol. wtof each individual component in the appropriate context. Thepresent version of the program produces results comparable witha human interpreter for some data. Band shifting and opticaldensity calculations are in a prototype form to permit evaluationof various techniques. Future work is directed at expandingthe system's capabilities to interpret data from other biologicalanalyses including DNA sequencing gels. Received on December 1, 1987; accepted on December 12, 1987     

X-Ray Diffraction of Myelin Membrane: II. Determination of the Phase Angles of the Frog Sciatic Nerve by Heavy Atom Labeling and Calculation of the Electron Density Distribution of the Membrane

The phase signs of the five main X-ray reflections from normal frog sciatic nerve have been determined as all positive using a technique of labeling with very small amounts of heavy metal. The changes in intensity of the individual reflections were studied as a function of uptake of metal label by the membrane. The possible localization of the metal label was decided from computer-analogue studies and from Patterson calculations. These phases are different from those determined by previous workers using techniques of trial of the best set of phases, or a step model, to give the best fit of the combined intensity data of normal and swollen myelin membranes. The electron density map has been calculated using eight reflections and their experimentally determined phases. The map shows an inner low electron density region which is different from that shown by earlier calculations. The center of the low electron density region shows a small region of increased electron density. However, without fixing absolute electron density levels in the map, it is not yet possible to allocate regions of low electron density to pure lipid or lipoprotein. The map shows the two sides of the membranes to be different in molecular structure without significant water spaces between the membranes.     

Automated protein model building combined with iterative structure refinement.

In protein crystallography, much time and effort are often required to trace an initial model from an interpretable electron density map and to refine it until it best agrees with the crystallographic data. Here, we present a method to build and refine a protein model automatically and without user intervention, starting from diffraction data extending to resolution higher than 2.3 A and reasonable estimates of crystallographic phases. The method is based on an iterative procedure that describes the electron density map as a set of unconnected atoms and then searches for protein-like patterns. Automatic pattern recognition (model building) combined with refinement, allows a structural model to be obtained reliably within a few CPU hours. We demonstrate the power of the method with examples of a few recently solved structures.     

VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams

VennPainter is a program for depicting unique and shared sets of genes lists and generating Venn diagrams, by using the Qt C++ framework. The software produces Classic Venn, Edwards’ Venn and Nested Venn diagrams and allows for eight sets in a graph mode and 31 sets in data processing mode only. In comparison, previous programs produce Classic Venn and Edwards’ Venn diagrams and allow for a maximum of six sets. The software incorporates user-friendly features and works in Windows, Linux and Mac OS. Its graphical interface does not require a user to have programing skills. Users can modify diagram content for up to eight datasets because of the Scalable Vector Graphics output. VennPainter can provide output results in vertical, horizontal and matrix formats, which facilitates sharing datasets as required for further identification of candidate genes. Users can obtain gene lists from shared sets by clicking the numbers on the diagram. Thus, VennPainter is an easy-to-use, highly efficient, cross-platform and powerful program that provides a more comprehensive tool for identifying candidate genes and visualizing the relationships among genes or gene families in comparative analysis.     

Closure of a genetic linkage map of human chromosome 7q with centromere and telomere polymorphisms.

We have constructed a 2.4-cM resolution genetic linkage map for chromosome 7q that is bounded by centromere and telomere polymorphisms and contains 66 loci (88 polymorphic systems), 38 of which are uniquely placed with odds for order of at least 1000:1. Ten genes are included in the map and 11 markers have heterozygosities of at least 70%. This map is the first to incorporate several highly informative markers derived from a telomere YAC clone HTY146 (locus D7S427), including HTY146c3 (HET 92%). The telomere locus markers span at least 200 kb of the 7q terminus and no crossovers within the physical confines of the locus were observed in approximately 240 jointly informative meioses. The sex-equal map length is 158 cM and the largest genetic interval between uniquely localized markers in this map is 11 cM. The female and male map lengths are 181 and 133 cM, respectively. The map is based on the CEPH reference pedigrees and includes over 4000 new genotypes, our previously reported data plus 29 allele systems from the published CEPH version 5 database, and was constructed using the program package CRI-MAP. This genetic linkage map can be considered a baseline map for 7q, and will be useful for defining the extent of chromosome deletions previously reported for breast and prostate cancers, for developing additional genetic maps such as index marker and 1-cM maps, and ultimately for developing a fully integrated genetic and physical map for this chromosome.     

Structure of the RNA in tobacco mosaic virus

A model of the RNA of tobacco mosaic virus has been built using computer model-building techniques. The model has good stereochemistry, and fits the electron density map of the virus obtained by fiber diffraction methods considerably better than did earlier models. The three sugar rings in the asymmetric unit all have the A (3′-endo) conformation, One of the bases is in the syn conformation, a conformation observed only rarely in nucleic acid structures.     

AiO,combining DNA/protein programs and oligo-management

SUMMARY: AiO (All in One) is a program for Windows, that combines typical DNA/protein features such as plasmid map drawing, finding of ORFs, translate, backtranslate and high quality printing with a number of databases. These databases allow the management of oligonucleotides, oligonucleotide-manufacturers, restriction enzymes, structural DNA and program users in a multi-user/multi-group environment. AVAILABILITY: An AiO specific website, with the possibility to download is at: http://134.99.88.55/aio/ SUPPLEMENTARY INFORMATION: Examples with screen shots- http://134.99.88.55/aio/ : Manual (in PDF format)-http://134.99.88.55/aio/manual.pdf