Computer program for calculating recombination values from electrophoretic data

A FORTRAN computer program was developed to calculate recombination values from F2 data. The input to the program is data on codominant alleles in any number of F2 families segregating for any number of loci, the limit being applied by the computer's memory capacity. For each pair of loci, regardless of the number of segregating progenies used, one recombination value is estimated by the method of maximum likelihood and reported with its standard error. In cases in which more than one family is used for the estimation, the chi-square for the homogeneity of the data also is reported.     

A program for maximum likelihood estimation and likelihood ratio tests in one-locus ABO-like systems based upon population phenotype data.

Phenotypes in an ABO-like system of a number of genetically-independent persons from a number of populations are supposed to be observed. The program which is written in FORTRAN calculates maximum likelihood estimates of gene frequencies and their standard errors in each population and in the populations taken together. Furthermore the program calculates expected values and likelihood ratio and goodness of fit chi-square tests of Hardy-Weinberg equilibrium. If several subpopulations are pooled together a likelihood ratio test of homogeneity is performed.     

A computer program for enzyme kinetics that combines model discrimination, parameter refinement and sequential experimental design.

A method of model discrimination and parameter estimation in enzyme kinetics is proposed. The experimental design and analysis of the model are carried out simultaneously and the stopping rule for experimentation is deduced by the experimenter when the probabilities a posteriori indicate that one model is clearly superior to the rest. A FORTRAN77 program specifically developed for joint designs is given. The method is very powerful, as indicated by its usefulness in the discrimination between models. For example, it has been successfully applied to three cases of enzyme kinetics (a single-substrate Michaelian reaction with product inhibition, a single-substrate complex reaction and a two-substrate reaction). By using this method the most probable model and the estimates of the parameters can be obtained in one experimental session. The FORTRAN77 program is deposited as Supplementary Publication SUP 50134 (19 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1986) 233, 5.     

Analysis of progress curves by simulations generated by numerical integration.

A highly flexible computer program written in FORTRAN is presented which fits computer-generated simulations to experimental progress-curve data by an iterative non-linear weighted least-squares procedure. This fitting procedure allows kinetic rate constants to be determined from the experimental progress curves. Although the numerical integration of the rate equations by a previously described method [Barshop, Wrenn & Frieden (1983) Anal. Biochem. 130, 134-145] is used here to generate predicted curves, any routine capable of the integration of a set of differential equations can be used. The fitting program described is designed to be widely applicable, easy to learn and convenient to use. The use, behaviour and power of the program is explored by using simulated test data.     

Algorithms for the search of amino acid patterns in nucleic acid sequences.

Some algorithms are described for the search of regions in a nucleic acid sequence that, when translated into amino acids, are homologous to a given amino acid pattern. All algorithms are modifications of the dynamic programming method for sequence comparison such that the translation of codons is taken into account. One of the algorithms has been implemented as a FORTRAN 77 program. The program operates on files that follow the format of the EMBL Nucleotide Sequence Data Library.     

Application of Fast Fourier Transform in Electroencephalography

Today the Fourier Transform is also used in the analysis of biological time series with periodical parts. For N = 2^M EEG sampling values the Fast Fourier Transform algorithm of COOLEY and TUKEY is applicable. For this a FORTRAN IV program EEG-FFT has been developed for computation of power spectrum. At the data processing equipment EC 1040 the CPU-time for 2¹⁰ = 1024 EEG sampling values is smaller than 1.5 s. The FORTRAN IV program can be applied both in offline and online data processing.     

A C version of Fourier-derived affinity spectrum analysis (FASA) to resolve binding heterogeneity

The computer program described in this paper facilitates resolutionof binding affinity heterogeneity by transforming binding curvedata (bound versus free) into affinity spectra (density versusaffinity). The original program, written in FORTRAN, is extendedand presented here in the language C. New applications includean ability to transform competition curves into affinity spectraand to evaluate the effects of sampling and experimental erroron spectrum analysis. We propose that this program be incorporatedin the routine evaluation of binding systems.     

Determination of initial velocities of enzymic reactions from progress curves.

The present communication describes a novel method for estimating initial velocities (v) of enzyme-catalysed reactions. It is based on an approximation of experimental data obtained by the cubic spline function. The initial velocity of a reaction is calculated as a derivative of the approximating function at a time value equal to zero. The proposed method is usable on a computer with a FORTRAN IV program. The method can be successfully used in such cases as substantial extents of substrate conversion, the inactivation of an enzyme in the course of a reaction, the existence of large experimental error or when the reaction mechanism is unknown.     

An automatic method for deriving steady-state rate equations.

A method is described for systematically deriving steady-state rate equations. It is based on the schematic method of King & Altman [J. Phys. Chem. (1956) 60, 1375-1378], but is expressed in purely algebraic terms. It is suitable for implementation as a computer program, and a program has been written in FORTRAN IV and deposited as Supplementary Publication SUP 50078 (12 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1977) 161, 1-2.     

Rapid initial clustering of large data sets

Summary Multivariate analysis of plant community data has three goals: summarization of redundancy, identification of outliers, and elueidation of relationships. The first two are handled conveniently by initial fast clustering, and the third by subsequent ordination and hierarchical clustering, and perhaps table arrangement.Initial clustering algorithms should achieve withincluster homogeneity and require minimal computer resources. However, algorithmic uniqueness and a hierarchy are not needed. Computing time should be proportional to the amount of data, with no higher dependencies on the number of samples. A method is presented here meeting these requirements, called composite clustering and implemented in a FORTRAN program called COMPCLUS. The computer time required for COMPCLUS clustering is on the order of the time required merely to read the data, regardless of the number of samples.Several large field data sets were analyzed effectively by using COMPCLUS to reduce redundancy and identify outliers, and then ordinating the resulting composite clusters by detrended correspondence analysis (DECORANA). Various clusterings of the same data set can be compared using a percent mutual matches (PMM) index, and a matrix of such values can be ordinated for simultaneous comparison of a number of clusterings.This paper benefited at many points from discussions with Mark O. Hill and Robert H. Whittaker. Mark Hill suggested condensed data storage. This work was done under a National Science Foundation grant to Robert Whittaker. I also appreciate technical assistance from Timothy F. Mason and Steven B. Singer.     

PEPCRE: an interactive program to create,manipulate and display oligopeptides

PEPCRE is an interactive computer graphics program for the rapid construction, manipulation and display of oligopeptides. Essentially any desired conformation of an oligopeptide can be constructed in a simple and straightforward manner. The program provides various display and output possibilities. It is user-friendly and is written in FORTRAN 77 for use on inexpensive, monochrome graphics terminals.     

Computer simulation of mutagenesis

A FORTRAN program is described which simulates point-substitution mutations in the DNA strands of typical organisms. Its objective is to help students to understand the significance and structure of the genetic code, and the mechanisms and effects of mutagenesis. The program is intended to be used as part of an elementary course in genetics at degree level.     

昆虫行为研究中日长的计算

提供了一种计算日长的算法及其FORTRAN77源程序。经过多年来在观测昆虫起飞行为、计算昆虫迁飞轨迹、确定昆虫临界光周期等行为学和生态学研究中的应用 ,表明该算法简单易行且具有足够的精度 (同于天文年历 ) ,是一种方便的实用工具     

STRAIN, a computer program for storing information about bacterial strains

Summary A FORTRAN computer program has been written which facilitates the storage of a large number of bacterial strains and their markers. With this program one can easily store, delete, add, and change data on strains and their markers and search for strains harboring desired markers.     

A computer aid for the preparation of Braun-Blanquet tables

Summary A non-clustering, FORTRAN IV computer program package for the preparation of phytosociological tables is described and examples of results are given. The advantages of being able to prepare camera-ready tables by this means are discussed.We thank Mr. D. van Eyssen for writing some of the computer programs and assisting with the processing.     

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).     

Interfacing similarity search software with the sequence retrieval system ACNUC

A method of interfacing sequence similarity search softwarewith the fast sequence retrieval system ACNUC is described.The method is written in FORTRAN 77 and is straightforward toimplement because no textprocessing code is required —a minimum of 12 extra lines of FORTRAN provided the interfacefor most applications. The method is also efficient, since sequencesare located by simple indexing techniques, with no linear searchesof large database files necessary. Received on November 20, 1986; accepted on January 8, 1987     

A FORTRAN Program for the KASTENBAUM-BOWMAN Test

The KASTEITBAUM -BOWMAN test allows the determination of the significance of a mutation frequency. A simple FORTRAN program for the KASTENBAUM -BOWMAN test is given. The subroutines may be incorporated easily into larger programs and allow to calculate the exact P value for the test.     

Matrix program to analyze primary structure homology

A FORTRAN program to analyze homology of letter strings (nucleotide or amino acid sequences) and to display the result in the form of a dot matrix is presented. The program is generally usable, user-friendly and has a number of options (filtering, "fudging," i.e., consideration of groups of homologous residues, and screening, i.e., display of only particular groups of residues) which greatly potentiate its analytical power.     

A new method for automatic metaphase finding adaptable to different chromosome preparations

A FORTRAN computer program, running on a Digital PDP 11-34 minicomputer, has been developed for use in conjunction with a Cambridge Quantimet 720 image analyzer for the investigation of metaphase preparations in routine cytogenetics. During a short initiation phase the program is adapted to the type of metaphase being analyzed. The program is fast and its performance is good, even at low microscopic magnifications. It has other uses in biology for all investigations and characterizations of small distinct elements widely spread within a preparation (e.g., autoradiography, bacteriology).