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At least 1,531 records · Page 85Linked to original sources
PubMed1987

A non-linear regression program in BASIC for estimating Km and Vmax.

This paper gives a program in BASIC for calculating the kinetic parameters Km and Vmax for an enzyme reaction from a set of paired values of reaction velocity at given substrate concentrations. An initial estimate of the two parameters is made using a weighted linear regression, these values are then used in an iterative process to fit the data to the Michaelis-Menten equation and give final values of Km and Vmax with their associated standard errors.

Algorithms↗
PubMed1987

Interfacing similarity search software with the sequence retrieval system ACNUC.

A method of interfacing sequence similarity search software with the fast sequence retrieval system ACNUC is described. The method is written in FORTRAN 77 and is straightforward to implement because no text-processing code is required--a minimum of 12 extra lines of FORTRAN provided the interface for most applications. The method is also efficient, since sequences are located by simple indexing techniques, with no linear searches of large database files necessary.

Algorithms↗
PubMed1988

A general purpose computer analysis system for chromatographic data.

A manual integration system for the analysis of chromatographic data is described. The analog output produced by an HPLC absorbance monitor is passed to a non-inverting signal amplifier. This amplified signal is sent to an IBM PC where an analog to digital converter is used to digitize the data. A set of six computer programs which collect, store and analyze these data are presented. This system was used to analyze the nucleotide content of the anaerobic organism Clostridium acetobutylicum by strong anion-exchange HPLC.

Algorithms↗
PubMed1988

Matrix algebra routines for the Acorn Archimedes microcomputer: example applications.

A set of matrix algebra routines have been written, as BASICV procedures, for the Acorn Archimedes microcomputer. It is shown that these procedures are executed so quickly that programs, which require matrix algebra computations, can be written in interpreted BASIC. Two example applications, reciprocal averaging and principal components analysis, are demonstrated.

Computers↗
PubMed1989

The frequency of oligonucleotides in mammalian genic regions.

The large body of nucleic acid sequence data now available offers a unique opportunity for the characterization of individual oligonucleotides which may be specific to sequence functional domains. We have prepared algorithms for the study of the frequency distribution of all oligonucleotides of length 2-6 in DNA sequences. We have implemented them in the study of 634 mammalian DNA sequences spanning 1.782 Mb, and have obtained the distribution of the ratio between the observed frequency of oligonucleotides and their expected frequency based on independent nucleotide probabilities. We then studied the distribution of oligonucleotides (or k-tuples) of each length in a subset of 129 complete mammalian genes spanning 0.607 Mb. Eight distinct genomic regions, namely 5'-non-transcribed, first exon, first intron, intermediate exons, intermediate introns, last intron, last exon and 3'-non-transcribed, were considered. We observed that some oligonucleotides show a statistical behaviour and a regional distribution similar to that of known signal sequences. Moreover the frequency distribution of oligonucleotides of length 5 and 6 tends to become bimodal, indicating the existence of a population of very frequent oligonucleotides.

Algorithms↗
PubMed1989

A new interactive protein sequence alignment program and comparison of its results with widely used algorithms.

A computer program that allows interactive sequence comparison is described. It graphically displays a search matrix using residue physiochemical characteristics and multilength segmental comparisons. The user selects through a mousing device and screen pointer the sequence spans to be matched. The results of this method are compared with those of ALIGN and BESTFIT.

Algorithms↗
PubMed1989

SED88: a Pascal program for the analysis of sedimentation equilibrium data.

Analytical ultracentrifugation is commonly used for the determination of molecular weights (sedimentation equilibrium) and sedimentation coefficients (sedimentation rate) of biological macromolecules in solution. A Turbo Pascal program for the analysis of sedimentation equilibrium centrifugation data produced by absorbance optical systems is described. The user may enter data from a scan of absorbance versus distance from the centre of rotation, via a graphics tablet (or ASCII file). This is subsequently manipulated to yield an apparent weight average molecular weight for the given sample. Plots of ln (absorbance) versus (radius2) may also be produced. The method described uses readily available computational equipment requiring only a graphics tablet in addition to an IBM PC compatible computer. This technique and the software developed have been used to investigate the molecular weight range of two International Humic Substances Society (IHSS) reference samples from the Suwannee River.

Absorption↗
PubMed1989

A BASIC program for the removal of noise from reaction traces using Fourier filtering.

Software for the removal of noise from reaction curves using the principle of Fourier filtering has been written in BASIC to execute on a PC. The program inputs reaction traces which are subjected to a rotation-inversion process, to produce functions suitable for Fourier analysis. Fourier transformation into the frequency domain is followed by multiplication of the transform by a rectangular filter function, to remove the noise frequencies. Inverse transformation then yields a noise-reduced reaction trace suitable for further analysis. The program is interactive at each stage and could easily be modified to remove noise from a range of input data types.

Algorithms↗
PubMed1989

A multiple sequence alignment algorithm for homologous proteins using secondary structure information and optionally keying alignments to functionally important sites.

The programs described herein function as part of a suite of programs designed for pairwise alignment, multiple alignment, generation of randomized sequences, production of alignment scores and a sorting routine for analysis of the alignments produced. The sequence alignment programs penalize gaps (absences of residues) within regions of protein secondary structure and have the added option of 'fingerprinting' structurally or functionally important protein-residues. The multiple alignment program is based upon the sequence alignment method of Needleman and Wunsch and the multiple alignment extension of Barton and Sternberg. Our application includes the feature of optionally weighting active site, monomer--monomer, ligand contact or other important template residues to bias the alignment toward matching these residues. A sum-score for the alignments is introduced, which is independent of gap penalties. This score more adequately reflects the character of the alignments for a given scoring matrix than the gap-penalty-dependent total score described previously in the literature. In addition, individual amino acid similarity scores at each residue position in the alignments are printed with the alignment output to enable immediate quantitative assessment of homology at key sections of the aligned chains.

Algorithms↗
PubMed1989

Fast and sensitive multiple sequence alignments on a microcomputer.

A strategy is described for the rapid alignment of many long nucleic acid or protein sequences on a microcomputer. The program described can handle up to 100 sequences of 1200 residues each. The approach is based on progressively aligning sequences according to the branching order in an initial phylogenetic tree. The results obtained using the package appear to be as sensitive as those from any other available method.

Algorithms↗
PubMed1989

Methods for calculating the probabilities of finding patterns in sequences.

This paper describes the use of probability-generating functions for calculating the probabilities of finding motifs in nucleic acid and protein sequences. Equations and algorithms are given for calculating the probabilities associated with nine different ways of defining motifs. Comparisons are made with searches of random sequences. A higher level structure--the pattern--is defined as a list of motifs. A pattern also specifies the permitted ranges of spacing allowed between its constituent motifs. Equations for calculating the expected numbers of matches to patterns are given.

Algorithms↗
PubMed1989

Exploring contingency tables with correspondence analysis.

An algorithm for correspondence analysis is described and implemented in SAS/IML (SAS Institute, 1985a). The technique is shown, through the analysis of several biological examples, to supplement the log-linear models approach to the analysis of contingency tables, both in the model identification and model interpretation stages of analysis. A simple two-way contingency table of tumor data is analyzed using correspondence analysis. This example emphasises the relationships between the parameters of the log-linear model for the table and the graphical correspondence analysis results. The technique is also applied to a three-way table of survey data concerning ulcer patients to demonstrate applications of simple correspondence analysis to higher dimensional tables with fixed margins. Finally, the diets and foraging behaviors of birds of the Hubbard Brook Forest are each analyzed and then a simultaneous display of the two separate but related tables is constructed to highlight relationships between the tables.

Algorithms↗
PubMed1989

A FORTRAN subroutine to compute inbreeding and kinship coefficients according to the number of ancestral generations.

This paper presents a FORTRAN IV subroutine to calculate inbreeding and kinship coefficients from pedigree information in a diploid population without self-fertilization. The user can specify the number of ancestral generations to be taken into account. It is thus possible to determine contributions of succeeding ancestral generations to the inbreeding and kinship coefficients under consideration. The subroutine is based on a recursive procedure that generates systematically all paths connecting two individuals. NP and NM, whose kinship coefficient is to be calculated (or between the father NP and the mother NM of the individual whose inbreeding coefficient is to be calculated). These paths obey the following conditions: (i) a given path does not contain the same parent-offspring link more than once; (ii) the vertex of a path is an ancestor common to individuals NP and NM, with a rank lower or equal to the parameter specified in input. Constraints regarding the size of the corpus of genealogical data and the storage method are discussed, as well as the interest of this subroutine compared to the existing ones. An example of application is given.

Algorithms↗
PubMed1989

TEFOOL/2: a program for theoretical drug design on microcomputers.

TEFOOL/2, a program written in BASIC, is presented in this paper. The purpose of TEFOOL/2 is to provide people interested in drug design with an easy-to-handle program where some of the most important techniques in QSAR are included. The program permits the selection of the training series, performs regression calculations and searches for optimum substituents. The latter is achieved by using either a Hansch's strategy or geometrical procedures. The program is interactive and can be implemented on an IBM-PC or compatible microcomputer. Although TEFOOL/2 has been developed for its application in drug design studies, its great flexibility makes it suitable for application to any experimental design or optimization process.

Algorithms↗
PubMed1989

Software tools for motif and pattern scanning: program descriptions including a universal sequence reading algorithm.

Two programs, MOTIF and PATTERN, that scan sequences for matches to user-defined motifs and patterns of motifs based on identity and set membership are described. The programs use a simple and logical notation to define motifs, and may be used either interactively or by using command line parameters (suitable for batch processing). The two programs described also incorporate a simple, yet reliable, algorithm that automatically detects in which of six possible formats the sequence entry is written.

Algorithms↗