A program to find regions of similarity between homologous protein sequences using dotmatrix analysis

MATRIX is a program designed primarily to enable the user to visualize all regions of similarity between two proteins at a glance. The program helps the user to see where they are similar—at what relative positions in the amino acid sequences of the two proteins in question does the similarity exist; how they are similar—what functional characteristics the two similar sequences have in common; and to what extent they are similar—is the similarity significant, if so how significant relative to other similar sequences in the protein. This is achieved by constructing a diagram in which quantitative parameters of amino acids are used to compare every amino acid residue of the first protein with every amino acid residue of the second.Another function of the program is, given two sets of atomic coordinates—either of different proteins or for the same protein (for self-comparison)—to demonstrate which residues of the two proteins, when the two proteins are superimposed upon each other, appear in the same space (or are close to each other).     

MolStruc: a force field calculation program allowing interactive modifications of the force field parameters

To analyze the influence of parameters and functions on the energy and geometry obtained through different force field calculations, we have developed program MolStruc. This software allows the user to choose between two sets of functions and parameters, MM2 and AMBER.The MM2 option of the program was developed to compute the coulombic energy in a dipole or monopole approximation. To establish comparisons between the energy values, the coulombic contribution is computed in the same way in the Amber and MM2 options of the program.The force field parameters can be handled interactively (through addition or modification).The program was used to study molecules of a representative sample displaying most of the problems encountered in molecular mechanics (MM).     

Multidimensional curve fitting program for biological data

A program written for use with the IBM-PC can be used to find least squares solutions to linearized multidimensional equations. The program is 'user-friendly' by requiring little from the user except to make decisions; most responses can be entered by a single keystroke. Once data are entered by the user, they can be repeatedly manipulated, graphed, and correlated. Many models relating data variables can be tried relatively easily, and best fit results found. Examples using respiratory mechanical data illustrate the ease of model comparisons.     

A large database DNA sequence handling program with generalized searching specifications.

The program described allows for the creation and manipulation of files of DNA sequence data up to very great lengths. The program uses its own paging system to load segments of the sequence into a small internal buffer so that the program does not have excessive memory requirements. The program offers a menu of functions to the user, and has been written to be forgiving of user errors. A code for the generalised specification of bases as a series of groups (i.e. A or T, Purine, etc.) has been devised and can be used in search specifications or in sequence files. Versions of the program have been developed to run with special efficiency under DIGITAL's RT11 operating system or to run under systems with a suitable implementation of FORTRAN VI.     

Datac: A multipurpose biological data analysis program based on a mathematical interpreter

The use of a mathematical command interpreter combined with the structural facility of the C-language allowed us to design a data treatment program having considerable flexibility and being able to handle any types of data (electrophysiological, biochemical and theoretical data). Ensembles of data are treated by the interpreter as if they were simple variables so that an elaborate computation can be performed on the spot by simply writing the appropriate equation on the terminal. These facilities combined with the ability of editing macrocommands at run time provide the user with data treatment possibilities that extends far beyond the possibilities actually implemented in the program. The originality of this program is that the user can easily implement the commands he most often needs, writing them in a language that most scientists will know, algebra.     

A simple computer program with statistical tests for the analysis of enzyme kinetics.

A simple computer program that calculates the kinetic parameters of enzyme reactions is described. Parameters are determined by nonlinear, least-squares regression using either Marquardt-Levenberg or Gauss-Newton algorithms to find the minimum sum of squares. Three types of enzyme reactions can be analyzed: single substrate reactions (Michaelis-Menten and sigmoidal kinetics), enzyme activation at a fixed substrate value or enzyme inhibition at a fixed substrate value. The user can monitor goodness of fit through nonparametric statistical tests (performed automatically by the computer) and through visual examination of the pattern of residuals. The program is unique in providing equations for activator and inhibition analysis as well as in enabling the user to fix some of the parameters before regression analysis. The simplicity of the program makes it extremely useful for quickly determining kinetic parameters during the data-gathering process.     

XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density

Xfit is a model-building and map viewing program in XtalView that is used by the structural biology community including researchers in the fields of crystallography, molecular modeling, and electron microscopy. Among its distinguishing features are built-in fast Fourier transforms that allow users flexibility in map calculations including the creation of OMIT maps and the updating of structure factors to reflect model changes from within the program. Written in C and using the freely available XView toolkit, it is highly portable to almost any X-windows based workstation including Intel-based LINUX systems. Its user interface is designed to aid in facile model-building and contains a semiautomated fitting system that allows the user to interactively and rapidly build chain de novo into an electron density map. The program is highly optimized to allow such features as interactive contour levels and map calculations to be completed within a few seconds. Features in the latest version including phase-combination, solvent-flattening, automated water addition, and small-probe dot contact surfaces, as well as basic design features, are discussed.     

A DNA sequence handling program

A computer program that aids in recording, editing, and analysis of the base sequences of DNA and RNA is presented. A tape containing copies of the program and the user manual for it are available at cost.     

An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences.

This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is displayed on a simple graphics terminal. Use of a graphics terminal allows the user to display the whole of the two sequences in one screenful or to home-in on regions of interest to examine them in more detail. The program is interactive and so the user can easily see the effect of changes to variables and can use inbuilt editing functions to make insertions to produce alignments of the two sequences. These aligned sequences can then be saved on disk files for further processing.     

A microcomputer based program for the storage and retrieval of experimental animal information

A microcomputer based program for the storage and selective retrieval of experimental animal information has been developed for use on any system which runs under CP/M system software. The program has been designed to be completely conversational, to communicate with the user in French, English, or Spanish, and to allow the user to define the data format and the alphanumeric coding scheme.     

A minicomputer program for automatic saccade detection and linear analysis of eye movement systems using sine wave stimulus

A FORTRAN IV program is described, which may be run interactively or in batch and which allows a user to obtain the frequency response amplitude ratio and phase resulting from the linear analysis of an eye movement system using sine wave stimuli. The response (eye position) signal may contain components contributed by the saccadic eye movements. The program can digitize analog signals and store data on a magnetic tape. With the aid of digital filters, the program can detect saccades without requiring any input parameters from the user. The program interpolates the saccade interval using a method of least square curve fitting with a sine wave. The interpolation is relatively noise immune and works well regardless of the stimulus frequencies and the width of a saccade interval. Moreover, the program can handle long duration of signals such as 90 min of data which covers about 5 cycles of a 0.001 Hz sine wave signal. Sample runs for the cases of 0.001 and 0.1 Hz are given. The resident driver and the overlayable segments of the program have been implemented on a DEC (Digital Equipment Corp.) LAB-11 minicomputer (PDP 11/20).     

GEOCHEM-EZ: a chemical speciation program with greater power and flexibility

GEOCHEM-EZ is a multi-functional chemical speciation program, designed to replace GEOCHEM-PC, which can only be used on DOS consoles. Chemical speciation programs, such as GEOCHEM and GEOCHEM-PC, have been excellent tools for scientists designing appropriate solutions for their experiments. GEOCHEM-PC is widely used in plant nutrition and soil and environmental chemistry research to perform equilibrium speciation computations, allowing the user to estimate solution ion activities and to consider simple complexes and solid phases. As helpful as GEOCHEM-PC has been to scientists, the consensus was that the program was not very user friendly, was difficult to learn and to troubleshoot, and suffered from several functional weaknesses. To enhance the usability and to address the problems found in GEOCHEM-PC, we upgraded the program with a Java graphical interface, added Help files, and improved its power and function, allowing it to run on any computer that supports Windows XP, Vista or Windows 7.     

Multi-user system for analysis of data from flow cytometry.

A new program is described for the analysis of DNA histograms from flow cytometry. The fundamental model representing the cell population is similar to one described previously. It assumes the population is grouped into compartments, each consisting of cells having approximately the same DNA content. After staining the cells with an appropriate fluorochrome, the fluorescence distribution of cells within each compartment is assumed to be Gaussian. In the present algorithm, the parameters of the model can either be computed directly by the program from the data, or can be specified as input by the user. When synchronous cell populations lacking distinct G1 and G2/M phases are analyzed, the parameter values must first be obtained using an appropriate control. Percentages of cells in the various compartments are computed using a gradient search method described by Bevington.     

Instructions for the CLONING program

These instructions for CLONING were developed to assist the user in understanding the operation of the program [Aldea and Kushner, Gene 65 (1988) 111-116]. The program provides a computational tool that performs cloning simulations using IBM PC/XT/AT or compatible microcomputers. The design of new recombinant molecules is a totally interactive process.     

DRAWNA: A program for drawing schematic views of nucleic acids

A program for drawing automatically exact and schematic views of nucleic acids is described. The program is written in C ANSI and uses the Silicon Graphics GL and Xirisw libraries within the X1 1/Motif environment. Through menus, the user can choose, specify, and manipulate in real time the three-dimensional views to be displayed. Drawing options include partitioning of structures into differently colored or shaped fragments, representation of backbones as flat or with conic-section ribbons, display of paired or free bases as rods, and display of surfaces as filled or outlined and stereo or depth-cued views.     

RFAC,a program for automated NMR R-factor estimation

A computer program (RFAC) has been developed, which allows the automated estimation of residual indices (R-factors) for protein NMR structures and gives a reliable measure for the quality of the structures. The R-factor calculation is based on the comparison of experimental and simulated ¹H NOESY NMR spectra. The approach comprises an automatic peak picking and a Bayesian analysis of the data, followed by an automated structure based assignment of the NOESY spectra and the calculation of the R-factor. The major difference to previously published R-factor definitions is that we take the non-assigned experimental peaks into account as well. The number and the intensities of the non-assigned signals are an important measure for the quality of an NMR structure. It turns out that for different problems optimally adapted R-factors should be used which are defined in the paper. The program allows to compute a global R-factor, different R-factors for the intra residual NOEs, the inter residual NOEs, sequential NOEs, medium range NOEs and long range NOEs. Furthermore, R-factors can be calculated for various user defined parts of the molecule or it is possible to obtain a residue-by-residue R-factor. Another possibility is to sort the R-factors according to their corresponding distances. The summary of all these different R-factors should allow the user to judge the structure in detail. The new program has been successfully tested on two medium sized proteins, the cold shock protein (TmCsp) from Termotoga maritima and the histidine containing protein (HPr) from Staphylococcus carnosus. A comparison with a previously published R-factor definition shows that our approach is more sensitive to errors in the calculated structure.     

质粒绘图软件PCircle的编制及Flash作为生物软件编制工具的可行性分析

以Flash作为软件编程工具 ,根据Flash在生物软件编制方面具有的优点 ,利用其优秀的图形图像处理能力与动作脚本语言 (ActionScript)相结合所具有的优势 ,编制了质粒绘图软件Pcircle。该软件克服了以往的质粒绘图软件在绘制图谱过程中不能随意修改操作的缺点 ,在绘制过程中 ,可在任意时候对生成的部件进行修改甚至删除。该软件已被生物软件网收录 ,供免费下载。同时详细分析了Flash作为生物软件编制工具所具有的优缺点 ,确定了作为生物软件编制工具的适用范围 ,可为Flash作为生物软件编制工具的使用起到指引作用。