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PubMed1991

Software for the development and evaluation of probabilistic identification matrices.

A number of programs are described for the development and evaluation of probabilistic identification matrices for use with computer-assisted identification. The program BEST reads an initial matrix of per cent probabilities for all the binary characters examined during a cluster analysis and determines the most useful set of tests for distinguishing taxa in the matrix. Program RESORT creates from the initial matrix an identification matrix in which the order of the tests may be different or the number of tests reduced. A printed version of a matrix can be produced by MATPRINT, which creates tables giving the per cent probability of a positive test result and the test results presented as '-', 'v' and '+' depending on a user-specified threshold. Program IDSC evaluates an identification matrix by calculating the best identification score for each taxon in the matrix using the expected result for each test. The programs were written in FORTRAN 77 and can be run on any micro-computer using the PC/MS-DOS operating system.

Algorithms↗
PubMed1991

PROMOT: a FORTRAN program to scan protein sequences against a library of known motifs.

Information about the three-dimensional structure or function of a newly determined protein sequence can be obtained if the protein is found to contain a characterized motif or pattern of residues. Recently a database (PROSITE) has been established that contains 337 known motifs encoded as a list of allowed residue types at specific positions along the sequence. PROMOT is a FORTRAN computer program that takes a protein sequence and examines if it contains any of the motifs in PROSITE. The program also extends the definitions of patterns beyond those used in PROSITE to provide a simple, yet flexible, method to scan either a PROSITE or a user-defined pattern against a protein sequence database.

Amino Acid Sequence↗
PubMed1991

Monte Carlo simulations of ionic channel selectivity.

Monte Carlo simulations have been developed to study the selectivity of ionic channels in biological membranes. The channel is considered to be in either of two possible states: (i) densely packed with ions, the ions moving in single file in one direction, or alternatively, (ii) sparsely packed, where holes could appear at any particular time thereby allowing bidirectional movement of ions. The two models enable us to envisage a quantitative flux of permeable ions in the presence of smaller sized ions, taking into consideration their concentrations in the bulk solutions, the ion-channel interactions and probability with which they fill up the channel. The programs are written in FORTRAN-77 (MS-FORTRAN) for an IBM-compatible personal computer. From the simulation results we observe an enzymatic function of the channel and also note that the smaller sized ions tend to block the movement of permeable ions. The simulations represent a technique for visualization of the factors that decide ionic permeability and help in manipulating their effects with ease and speed which would otherwise involve intricate experimental setups.

Algorithms↗
PubMed1991

MCS/SEL/BAS program--an overlapping clustering method with examples from mating type interactions of ciliated protozoa.

The MCS/SEL/BAS program provides a method for group recognition, based on a criterion of homogeneity within the groups. The basic aim of this clustering method is not to 'force' data into a number of separate groups, as it allows the possibility that a given element in the data set can be assigned to more than one group. Moreover, a parsimonious path through the groups is sought by selecting groups on the basis of two suitably chosen, peak-ordered criteria. This selection continues until a covering of the data set is obtained (i.e., until each element in the data set is assigned to at least one group). Then relationships occurring among the set of selected groups are investigated by means of two coefficients, called overlapping and cohesion coefficient, respectively. The utility of this program has been demonstrated here in elaborating large sets of data derived from mating type interactions of ciliates, but it can be used also for analyzing data derived from a wide spectrum of compatibility phenomena exhibited by other living organisms. Algorithms of this program are written in BASIC and formulated in a conversational mode for processing on a Macintosh. A computer program (MCS/SEL/BAS) is available from G. Mancini upon request.

Algorithms↗
PubMed1991

A simple approach for the distribution of computationally intense tasks in an heterogeneous environment: distribution of the MDPP image-processing package.

A method has been developed to link the display ability of a high-resolution graphics workstation with the computational power of a local mainframe or a remote supercomputer via an electronic data network. The method allows this link to be established in a manner largely transparent to the user. The application of the method is illustrated by our successful distribution of the computationally intensive portions of an imaging program (MDPP) from a small VAX workstation to a VAX mainframe and Cray Y-MP8/832 using a simple message-passing technique. This technique can be applied to almost any configuration of networked machines.

Algorithms↗
PubMed1992

IBIS integrated biological imaging system: electron micrograph image-processing software running on Unix workstations.

'IBIS' is a set of computer programs concerned with the processing of electron micrographs, with particular emphasis on the requirements for structural analyses of biological macromolecules. The software is written in FORTRAN 77 and runs on Unix workstations. A description of the various functions and the implementation mode is given. Some examples illustrate the user interface.

Computer Systems↗
PubMed1993

Microcomputer BASIC programs for rapid determination of lethal dosages of biocides using logit transformations.

The probit analysis model is generally used for the determination of lethal dosages in bioassay applications. However, the logit models, which use the logistic curve instead of the integrated normal curve, could also be effectively used for the determination of lethal dosages and regression coefficients. In this paper, two types of logit models, namely minimum logit chi square and maximum likelihood, have been described in detail for the estimation of the parameters. The results of these two models are also compared with those of the probit model.

Animals↗
PubMed1993

Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed.

A refined algorithm together with a computer procedure for determining the complete set of non-negative, steady-state fluxes in biochemical reaction systems of any complexity, with or without some flux rates fixed, is given. It is shown that this set is a convex polyhedron, which may or may not be bounde. The algorithm is illustrated by several examples; one of them concerns intermediary metabolism. A computer code in standard C is presented.

Algorithms↗
PubMed1993

An algorithm for the identification of similar oligopeptides between amino acid sequences.

Molecular mimicry is the origin of common structural patterns in sequences of viral and host proteins, and it appears to be related to the development of autoimmune diseases. The identification of structural molecular similarities among viral and host proteins is thus very relevant in the development of engineered antiviral vaccines to avoid potentially dangerous effects. In this respect identifying pairs of similar oligopeptides between given proteins, independently of the overall degree of similarity of their amino acid sequences, is of interest. To this aim we have designed and implemented an algorithm capable of finding and classifying (with respect to their statistical significance) all possible pairs of similar oligopeptides between two proteins irrespective of length, number, location and ordering of the pairs along the sequences. The algorithm is very efficient and much more suited for this kind of local search than standard alignment programs. The latter, dealing with the sequences as a whole, are, in these cases, of very limited applicability. We have used the algorithm to compare a glycoprotein of the human immunodeficiency virus (HIV) type 1 and with the beta-chains of human leukocyte antigen (HLA). Besides a previously identified peptide, we have found a new peptide located in the fusion site of HIV that shares high similarity with the transmembrane domains of HLA.

Algorithms↗
PubMed2025

Parsing GTF and FASTA files using the eccLib Library.

SUMMARY: Leveraging the Python/C API, eccLib was developed as a high-performance library designed for parsing genomic files and analysing genomic contexts. To the best of the authors' knowledge, it is the fastest Python-based solution available. With eccLib, users can efficiently parse GTF/GFFv3 and FASTA files and utilize the provided methods for additional analysis. AVAILABILITY AND IMPLEMENTATION: This library is implemented in C and distributed under the GPL-3.0 licence. It is compatible with any system that has the Python interpreter (CPython) installed. The use of C enables numerous optimizations at both the implementation and algorithmic levels, which are either unachievable or impractical in Python.

Software↗
PubMed2003

MuGeN: simultaneous exploration of multiple genomes and computer analysis results.

MOTIVATION: The availability of increasing amounts of sequence data about completely sequenced genomes spurs the development of new methods in the fields of automated annotation, and of comparative genomics. Tools allowing the visualization of results produced by analysis methods, superimposed on possibly annotated sequence data, and enabling synchronized navigation in multiple genomes, provide new means for interactive genome exploration. This kind of visual inspection can be used as a basis to assess the quality of new analysis algorithms, or to discover genome portions to be subjected to in-depth studies. RESULTS: We propose a software package, MuGeN, built for navigating through multiple annotated genomes. It is capable of retrieving annotated sequences in several formats, stored in local files, or available in databases over the network. From these, it then generates an interactive display, or an image file, in most common formats suitable for printing, further editing or integrating in Web pages. Genome maps may be mixed with computer analysis results loaded from XML files, whose format is generic enough to be adapted to a majority of sequence oriented analysis methods. AVAILABILITY: MuGeN is available at http://www-mig.jouy.inra.fr/bdsi/MuGeN.

Computer Graphics↗
PubMed2003

FPV: fast protein visualization using Java 3D.

MOTIVATION: Many tools have been developed to visualize protein structures. Tools that have been based on Java 3D((TM)) are compatible among different systems and they can be run remotely through web browsers. However, using Java 3D for visualization has some performance issues with it. The primary concerns about molecular visualization tools based on Java 3D are in their being slow in terms of interaction speed and in their inability to load large molecules. This behavior is especially apparent when the number of atoms to be displayed is huge, or when several proteins are to be displayed simultaneously for comparison. RESULTS: In this paper we present techniques for organizing a Java 3D scene graph to tackle these problems. We have developed a protein visualization system based on Java 3D and these techniques. We demonstrate the effectiveness of the proposed method by comparing the visualization component of our system with two other Java 3D based molecular visualization tools. In particular, for van der Waals display mode, with the efficient organization of the scene graph, we could achieve up to eight times improvement in rendering speed and could load molecules three times as large as the previous systems could. AVAILABILITY: EPV is freely available with source code at the following URL: http://www.cs.ucsb.edu/~tcan/fpv/

Computer Graphics↗
PubMed2003

Genome visualization made fast and simple.

SUMMARY: The easiest way to gain a quick overall understanding of genomic data is with a visual display that allows the user to view information about an entire genome or chromosome at once. We have constructed GenomePlot, a Perl/Tk script with a series of modules that allow us to display many types of information simultaneously. Menu options allow the user to zoom to the desired view of the data and to print or save the image to a file to produce publication quality illustrations. AVAILABILITY: The program is available on request. A license is required for commercial use.

Algorithms↗