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PubMed1990

The development of a high-order Taylor expansion solution to the chemical rate equation for the simulation of complex biochemical systems.

A numerical method for evaluating chemical rate equations is presented. This method was developed by expressing the system of coupled, first-degree, ordinary differential chemical rate equations as a single tensor equation. The tensorial rate equation is invariant in form for all reversible and irreversible reaction schemes that can be expressed as first- and second-order reaction steps, and can accommodate any number of reactive components. The tensor rate equation was manipulated to obtain a simple formula (in terms of rate constants and initial concentrations) for the power coefficients of the Taylor expansion of the chemical rate equation. The Taylor expansion formula was used to develop a FORTRAN algorithm for analysing the time development of chemical systems. A computational experiment was performed with a Michaelis-Menten scheme in which step size and expansion order (to the 100th term) were varied; the inclusion of high-order terms of the Taylor expansion was shown to reduce truncation and round-off errors associated with Runge-Kutta methods and lead to increased computational efficiency.

Algorithms↗
PubMed1990

Generating precise mechanical stimuli and recording chordotonal organ discharge patterns using a microcomputer.

A computer-controlled system for the investigation of the response properties of the tibio-femoral chordotonal organ in the locust is described. The computer is used to generate small amplitude sinusoidal movements of the tibia via a small servo-controlled motor. The resulting response recorded via a suction electrode is simultaneously detected, processed and stored on disk. Full constructional details for all hardware required are given. The software, developed for a BBC microcomputer, in addition to controlling all the hardware, has graphics and analysis routines enabling the operator to display and manipulate the stored data.

Action Potentials↗
PubMed1990

A set of programs for analysis of kinetic and equilibrium data.

A program package that can be used for analysis of a wide range of kinetic and equilibrium data is described. The four programs were written in Turbo Pascal and run on PC, XT, AT and compatibles. The first of the programs allows the user to fit data with 16 predefined and one user-defined function, using two different non-linear least-squares procedures. Two additional programs are used to test both the evaluation of model functions and the least-squares fits. One of these programs uses two simple procedures to generate a Gaussian-distributed random variable that is used to simulate the experimental error of measurements. The last program simulates kinetics described by differential equations that cannot be solved analytically, using numerical integration. This program helps the user to judge the validity of steady-state assumptions or treatment of kinetic measurements as relaxations.

Algorithms↗
PubMed1990

Quantitative analysis of the selective pressure exerted on homologous proteins.

Evolution analysis is used to locate the regions of a protein that are important for its function or structure. The rate of evolution is generally constant for a given family of homologous sequences. From the starting point of this observation, an algorithm is proposed to establish quantitatively the sequence zones where selective pressure is maximal. A program that computes this pressure has been written in PASCAL. Analysis of results on some sequences validate this theoretical approach, and this knowledge can be used as a starting-point for carrying out site-directed mutagenesis.

Algorithms↗
PubMed1990

POLCA, a library running in a modern environment, implements a protocol for averaging randomly oriented images.

The library POLCA implements the averaging of biological structures whose images are recorded in digital form from electron micrographs. The averaging protocol is based upon a method developed about ten years ago, which allows one to operate on a sequence of objects oriented and displaced at random within their frame; the relative rotations and the displacements of the structures are detected with the use of correlation algorithms and modified to make all objects appear the same, apart from their noisy components. The average image is then obtained by a simple addition and the signal-to-noise ratio is improved by a factor equal to the square root of the number of objects used to calculate the average. With respect to the original implementation of the method, two novel features characterize the library: the first one deals with the functions that are cross-correlated to determine the relative rotations of the structures; the functions used here are the inverse transforms of the amplitude spectra (IAS functions), which give rise to sharp maxima when they are cross-correlated. The second peculiarity is the systematic adoption, in the transformations of coordinates and in other circumstances, of an interpolation technique based upon the Fourier series kernel. POLCA is written in C and runs on a VME machine under the UNIX V/68 operating system. A programming style has been adopted to exploit fully the machine resources.

Algorithms↗
PubMed1990

Exact computation of pattern probabilities in random sequences generated by Markov chains.

Observed patterns in macromolecular sequences are often considered as words and compared with their probabilities of occurring in random sequences. Calculation of these probabilities, however, often lacks rigour. We have developed an algorithm for exact computation of such probabilities for stochastic sequences that follow a Markov chain model. The method is applicable to the case that a random sequence contains one out of two given patterns P and Q, or both simultaneously. Another application yields the probability function P(x) that a sequence contains pattern P exactly x times. An application to patterns that include wild-card characters yields probabilities for homonucleotide clusters of a given length. We prove the probability of multiple runs of single nucleotides in the SV40 genome to be in accordance with the dinucleotide composition of the sequence, although it is in conflict with mononucleotide composition.

Algorithms↗
PubMed1990

Automatic computation of enzyme kinetics by HPLC.

Enzyme activity can be easily measured by HPLC using traces of the product itself as an internal standard. Our procedure involved the development of an equation using the experimental data obtained in the kinetic assay. The entire procedure can thus be automated and a computer program is presented here for facilitating the assay and saving time. The determination of the activity of NAD kinase is reported as an example.

Algorithms↗
PubMed1991

Genome inhomogeneity is determined mainly by WW and SS dinucleotides.

According to the hypothesis of the modular structure of DNA, genomes consist of modules of various nature which may differ in statistical characteristics. Statistical analysis helps in revealing the differences in statistical characteristics and predicting the modular structure. In this connection the question about the contribution of each word of length l (l-tuple) to the inhomogeneity of genetic text arises. The notion of stationary (i.e. relatively evenly distributed over a genome) versus non-stationary l-tuples has been introduced previously. In this paper, the dinucleotide distributions for all long sequences from GenBank were analyzed and it was shown that non-stationary dinucleotides are closely associated with polyW and polyS tracts (W denotes 'weak' nucleotides A or T, while S stands for the 'strong' nucleotides G or C). Thus, genome inhomogeneity is shown to be determined mainly by AA, TT, GG, CC, AT, TA, GC and CG dinucleotides. It has been demonstrated that neither 'codon usage' nor the 'isochore model' can account for this phenomenon.

Algorithms↗
PubMed1991

A simulation program to display specific digestion products of predicted RNA foldings.

A parameterizable program in Pascal was developed for VAX/VMS computers to simulate the autoradiograms of gel-separated RNA fragments generated by partial cleavage of a folded RNA molecule using five specific RNases. Each screen displays the results of cleavage by either one enzyme or all five, with the RNA molecule labeled at either of its ends (5' or 3'); each run is performed with three different lengths and against a ladder containing alkaline hydrolysis products of the same RNA molecule as size markers. The program should be useful for comparing actual results with predicted functional foldings of RNA molecules.

Algorithms↗
PubMed1991

Scanning protein sequence databanks using a distributed processing workstation network.

The programme pscan has been developed to distribute protein databank scans over a network of computers that share a common file system. pscan may be used in conjunction with most conventional sequence comparison programmes with few modifications. In test runs using the Smith-Waterman dynamic programming algorithm, the time required to scan a 6858 sequence databank using a query sequence 740 residues long was reduced from approximately 50 min for a single processor, to approximately 11 minutes for five processors. Accordingly, pscan provides a low-cost, portable alternative to dedicated parallel processing computers.

Algorithms↗
PubMed1991

PASHEMOS: a versatile program written in Pascal to simulate patterns on the shells of molluscs, according to the Meinhardt model.

In this paper we describe PASHEMOS, a user-friendly program written in Pascal to solve the Meinhardt-Klingler model numerically. This model studies the shell pattern pigmentation of molluscs. Moreover, PASHEMOS enables theoretical analysis to be performed on the different steady states. The program takes into account the four differential equation systems established in the model. It numerically solves these systems. This program is developed in such a way that both the equation system type and the parameter values can be chosen. The pattern is displayed in each case, and other output possibilities are available (i.e. three-dimensional concentration plotting, phase plane, phase space, stability analysis). The implementation of the program for the case of a three-variable system is shown as an example of PASHEMOS handling. Program applications for other models are also discussed.

Algorithms↗