PERFILS: a program for the quantitative treatment of footprinting data

PERFILS, a computer program written in Borland TurboPascal,performs quantitative analysis of footprinting experiments usingany IBM PC or compatible microcomputer. The program uses theheight of the bands obtained from densitometric scanning offootprinting autoradiographs to calculate a differential cleavageplot. Such a plot displays, on a logarithmic scale, the differenceof susceptibility of a DNA fragment to DNase I, or any othercleaving agent, in the presence of any ligand versus the sequence.PERFILS calculates the fractional cleavage values for controland ligand, giving a table of values for each internucleotidicbond and rendering the differential cleavage plot in only afew seconds.     

A note on the measurement of redundancy

Plant Ecology - The present paper points out a simpler method for computing the redundancy coefficient proposed by Orlóci (1975) using the inverse of the variance-covariance matrix. It is...     

DESIGN: computerized optimization of experimental design for estimating Kd and Bmax in ligand binding experiments. I. Homologous and heterologous binding to one or two classes of sites

We have developed a versatile computer program for optimization of ligand binding experiments (e.g., radioreceptor assay system for hormones, drugs, etc.). This optimization algorithm is based on an overall measure of precision of the parameter estimates (D-optimality). The program DESIGN uses an exact mathematical model of the equilibrium ligand binding system with up to two ligands binding to any number of classes of binding sites. The program produces a minimal list of the optimal ligand concentrations for use in the binding experiment. This potentially reduces the time and cost necessary to perform a binding experiment. The program allows comparison of any proposed experimental design with the D-optimal design or with assay protocols in current use. The level of nonspecific binding is regarded as an unknown parameter of the system, along with the affinity constant (Kd) and binding capacity (Bmax). Selected parameters can be fixed at constant values and thereby excluded from the optimization algorithm. Emphasis may be placed on improving the precision of a single parameter or on improving the precision of all the parameters simultaneously. We present optimal designs for several of the more commonly used assay protocols (saturation binding with a single labeled ligand, competition or displacement curve, one or two classes of binding sites), and evaluate the robustness of these designs to changes in parameter values of the underlying models. We also derive the theoretical D-optimal design for the saturation binding experiment with a homogeneous receptor class.     

Non-linear fitting program for biological data

A simple microcomputer program written in Microsoft Basic estimates pharmacokinetic parameters using the coordinate search technique to minimize the sum of squared errors. The program developed for portable computers combines a plot of data and curve fitting so as to find rapidly the initial parameters with the subsequent optimization of the parameter estimate.     

A Fisher scoring algorithm for the weighted regression method of QTL mapping

An improved weighted least square (LS) method for quantitative trait loci (QTL) mapping using the estimating equation (EE) algorithm was developed recently. The method is more efficient than both the LS and the weighted LS methods and slightly less efficient than the mixture model maximum likelihood (ML) method. The iteration process of the EE algorithm is implicit. We developed a Fisher-scoring algorithm for the weighted LS method. The iteration process is explicit and easy to program. In addition, the method automatically provides an approximate variance-covariance matrix for the estimated QTL parameters as a by-product of the iteration process. As a consequence, a W-test statistic can be used for testing the significance of QTL. To compare the Fisher scoring algorithm with the expectation maximization (EM)-based ML method, we also developed a slightly simplified method to compute the variance-covariance matrix of the estimated parameters under the EM algorithm.     

Comprehensive restriction enzyme lists to update any DNA sequence computer program

Restriction enzyme lists are presented for the practical working geneticist to update any DNA computer program. These lists combine formerly scattered information and contain all presently known restriction enzymes with a unique recognition sequence, a cut site, or methylation (in)sensitivity. The lists are in the shortest possible form to also be functional with small DNA computer programs, and will produce clear restriction maps without any redundancy or loss of information. The lists discern between commercial and noncommercial enzymes, and prototype enzymes and different isoschizomers are cross-referenced. Differences in general methylation sensitivities and (in)sensitivities against Dam and Dcm methylases of Escherichia coli are indicated. Commercial methylases and intron-encoded endonucleases are included. An address list is presented to contact commercial suppliers. The lists are constantly updated and available in electronic form as pure US ASCII files, and in formats for the DNA computer programs DNA-Strider for Apple Macintosh, and DNAsis for IBM personal computers or compatibles via e-mail from the internet address: netservembl-heidelberg.de by sending only the message help relibrary.     

NKCELPRO: a program for microcomputer applicable to the study of responses of spontaneous cytotoxicity

A microcomputer program (NKCELPRO) which expedites the exact quantification of various parameters referring to NK cell activities is described. The program is written in BASIC language and computes the activities of cell-mediated cytotoxicity by collating and reducing radioactive count data obtained from 51Cr releasing assays. The information generated by this program includes statistics such as the average values, fitting by last square regression line with its correlation coefficient, as well as determination of the percent specific lysis and lytic units/10(7) effector cells according to any reference value previously defined by the operator. Special program features allow for a certain flexibility in the experimental protocol design as well as in the graphic expression of the results. Data storage on a disk with filing purposes for subsequent studies is also available.     

DNA sequence analysis: a procedure to find homologies among many sequences.

SEQCMP, a program that analyzes and searches for homology among multiple nucleic acid sequences, is described. The sequences are compared by the dot matrix method and the consensus sequence is derived by superimposing all the dot matrices on one another. The program is written in MBASIC and runs on IBM-PC microcomputer. It is interactive and can be used by investigators with no computer background or experience.     

Evaluation of the jackknife technique for fitting multiexponential functions to biochemical data

The jackknife technique was tested by fitting a two-exponential function to the time course of disappearance of radioactivity from the area of a wheat leaf that had been fed ¹⁴CO₂. The function was fitted by both unweighted and weighted least squares, first without and then with the jackknife. Weighting altered the estimates of the function's parameters, but jackknifing did not. Hence jackknifing did not remove any of the bias introduced by incorrect weighting. The confidence limits of the parameters calculated by jackknifing were greater than those estimated from the variance-covariance matrix of the regression, but similar to those derived from replicate experiments. The jackknife also allowed confidence limits for the rate constants and transit time of the underlying two-compartment model to be derived.     

Computation of the sedimentation coefficient, S0(20),w, from the analytical ultracentrifuge run by an interactive program on the Apple II microcomputer

We have developed a computer program for the calculation of the sedimentation coefficient of a macromolecule from the raw data collected from an analytical ultracentrifuge run. The program is written for the Apple II microcomputer and is capable of calculating the sedimentation coefficient at an infinite dilution from the data collected at varying concentrations.     

Computation of the sedimentation coefficient,s20,w0, from the analytical ultracentrifuge run by an interactive program on the Apple II microcomputer

We have developed a computer program for the calculation of the sedimentation coefficient of a macromolecule from the raw data collected from an analytical ultracentrifuge run. The program is written for the Apple II microcomputer and is capable of calculating the sedimentation coefficient at an infinite dilution from the data collected at varying concentrations.     

HOMOGENEITY OF THE GENETIC VARIANCE-COVARIANCE MATRIX FOR ANTIPREDATOR TRAITS IN TWO NATURAL POPULATIONS OF THE GARTER SNAKE THAMNOPHIS ORDINOIDES

Quantitative genetic models of evolution rely on the genetic variance-covariance matrix to predict the phenotypic response to selection. Both prospective and retrospective studies of phenotypic evolution across generations rely on assumptions about the constancy of patterns of genetic covariance through time. In the absence of robust theoretical predictions about the stability of genetic covariances, this assumption must be tested with empirical comparisons of genetic parameters among populations and species. Genetic variance-covariance matrices were estimated for a suite of antipredator traits in two populations of the northwestern garter snake, Thamnophis ordinoides. The characters studied include color pattern and antipredator behaviors that interact to facilitate escape from predators. Significant heritabilities for all traits were detected in both populations. Genetic correlations and covariances were found among behaviors in both populations and between color pattern and behavior in one of the populations. Phenotypic means differed among populations, but pairwise comparisons revealed no heterogeneity of genetic parameters between the populations. The structure of the genetic variance-covariance matrix has apparently not changed significantly during the divergence of these two populations.     

A computer program for the estimation of protein and nucleic acid sequence diversity in random point mutagenesis libraries

A computer program for the generation and analysis of in silico random point mutagenesis libraries is described. The program operates by mutagenizing an input nucleic acid sequence according to mutation parameters specified by the user for each sequence position and type of point mutation. The program can mimic almost any type of random mutagenesis library, including those produced via error-prone PCR (ep-PCR), mutator Escherichia coli strains, chemical mutagenesis, and doped or random oligonucleotide synthesis. The program analyzes the generated nucleic acid sequences and/or the associated protein library to produce several estimates of library diversity (number of unique sequences, point mutations, and single point mutants) and the rate of saturation of these diversities during experimental screening or selection of clones. This information allows one to select the optimal screen size for a given mutagenesis library, necessary to efficiently obtain a certain coverage of the sequence-space. The program also reports the abundance of each specific protein mutation at each sequence position, which is useful as a measure of the level and type of mutation bias in the library. Alternatively, one can use the program to evaluate the relative merits of preexisting libraries, or to examine various hypothetical mutation schemes to determine the optimal method for creating a library that serves the screen/selection of interest. Simulated libraries of at least 10⁹ sequences are accessible by the numerical algorithm with currently available personal computers; an analytical algorithm is also available which can rapidly calculate a subset of the numerical statistics in libraries of arbitrarily large size. A multi-type double-strand stochastic model of ep-PCR is developed in an appendix to demonstrate the applicability of the algorithm to amplifying mutagenesis procedures. Estimators of DNA polymerase mutation-type-specific error rates are derived using the model. Analyses of an alpha-synuclein ep-PCR library and NNS synthetic oligonucleotide libraries are given as examples.     

A Model for the Regulation of K Influx, and Tissue Potassium Concentrations by Negative Feedback Effects upon Plasmalemma Influx

By means of a modified Michaelis-Menten equation for K⁺ influx, which includes terms for root and external K⁺ concentrations (root [K⁺] and [K⁺]₀, respectively) it is possible to predict the manner in which short-term (perturbation) fluxes of K⁺ into roots of barley plants (Hordeum vulgare cv Fergus) vary with root [K⁺] and [K⁺]₀. Influx values derived from this equation were used to predict changes of root and shoot [K⁺] and K⁺ absorption rates (as functions of time and [K⁺]₀) from a knowledge of K⁺ efflux, relative growth rates of roots and shoots, and the partitioning of absorbed K⁺ between these organs. A microcomputer program was employed to model these changes in low-salt plants following transfer to solutions in which [K⁺]₀ was maintained at values ranging from 5 to 1000 millimoles per cubic meter. The model was operated on the basis of 10 minute absorption periods which provided data for continuous `updating' of tissue [K⁺]. The simulations were undertaken for periods corresponding to 30 days. During this time the model accurately predicted the manner in which K⁺ influx and root and shoot [K⁺] gradually approach values which are essentially independent of [K⁺]₀. The computer program was also used to predict the outcome of changing various external and internal parameters of the proposed regulatory system. The results of these simulations are discussed in the context of current models for negative feedback control of ion fluxes.     

Development of a program package for modelling biochemical systems

The development of a program for the identification of a model including up to 15 compartments is presented. The identification of the model parameters with this program package is based upon the improved Gauss Marquardt algorithm. This program, implemented on a microcomputer (Data General) Eclipse 64 K RAM), uses a calculation and automatic generation of a partial derivative routine. Thus, starting from the differential equations of the model correctly written, there is no longer any risk of error.     

Microcomputer simulation of steady-state enzyme kinetics for educational purposes

A BASIC program to assist the instruction of steady-state enzymekinetics has been developed for the IBM PC microcomputer. Itspurpose is to simulate laboratory experiments in order to minimizethe time required to obtain kinetic data from which studentsdeduce kinetic mechanisms and determine kinetic constants ofenzyme-catalyzed reactions. The program randomly selects a kineticscheme from various sequential, ping pong, and iso reactionsequences as well as values for the kinetic constants. The schemeand kinetic constants are unknown to the student at this time;the only thing he or she knows is the stoichiometry of the catalyzedreaction which can have two or three substrates and products.The student is prompted to enter values for concentrations ofsubstrates and products; several different concentrations foreach substrate and product can be entered in a single experiment.The program then calculates, displays and prints (if desired)the corresponding initial steadystate velocities. The studentcan perform as many experiments as desired until enough informationis obtained to determine the kinetic mechanism and to calculatevalues for the kinetic constants. Received on March 10, 1986; accepted on May 6, 1986     

The Calculation of Parameters of the Moffitt Equation for Rotatory Dispersion Data

The least squares calculation of the best values of the parameters of the Moffitt equation and of the Drude equation is examined. It is proved that the least squares evaluation of all three parameters of the Moffitt equation becomes indeterminate as the b_o term approaches zero. Estimates of low helical content based on the Moffitt relationship are therefore also indeterminate and of dubious value. Both the size of b_o and the range of wavelengths chosen affect the standard deviations of the parameters. The magnitude of the effects is illustrated by selected examples. The computer program OPTROT is available for evaluating the extent to which data may be correlated by the equations.     

Formulas predicting survival in patients with heart transplantation

Kirklin et al. (J Heart Transpl, 7 (1988) 331–336) reported survival data in 132 patients who underwent heart transplantation. Survival was evaluated by using the product-limit method of Kaplan-Meier and maximum likelihood method. In addition, the effect of pulmonary vascular resistance on survival was estimated by using multivariate analysis. A microcomputer program in BASIC for predicting the survival probability after transplantation in patients with heart transplantation is designed. The formula used in this program is derived from the survival data reported by Kirklin et al. (J Heart Transpl, 7 (1988) 331–336). A mathematical model of the ‘probacent’-probability equation and a computer program previously published by the author are employed in this study. Analysis of the computer-assisted predicted values and the data reported by Kirklin et al. (J Heart Transpl, 7 (1988) 331–336) indicates that the program is accurate and reliable with a complete agreement in expressing survival probability as a function of time after heart transplantation. The computer-assisted predictive formula can determine the relationship between the time and the survival probability and may be of value for prognostic evaluation of patients. The computer-assisted mathematical model of the ‘probacent’-probability equation may be proposed as a general approximation method to make useful predictions of probable outcomes in various biomedical phenomena.     

A microcomputer program for analysis of nucleic acid hybridization data

The study of nucleic acid hybridization is facilitated by computer mediated fitting of theoretical models to experimental data. This paper describes a non-linear curve fitting program, using the `Patternsearch' algorithm, written in BASIC for the Apple II microcomputer. The advantages and disadvantages of using a microcomputer for local data processing are discussed.