A flexible new computer program for handling DNA sequence data.

A compact new computer program for handling nucleic acid sequence data is presented. It consists of a number of different subsets, which may be used according to a given code system. The program is designed for the determination of restriction enzyme and other recognition sites in correlation with translation patterns, and allows tabulation of codon frequencies and protein molecular weights within specified gene boundaries. The program is especially designed for detection of overlapping genes. The language, is FORTRAN and thus the program may be used on small computers; it may also be used without any prior computer experience. Copies are available on request.     

BRAGI: A comprehensive protein modeling program system

A protein modeling program package has been developed. The user friendly system is implemented on high performance graphic devices and facilitates the modeling of a protein with an unknown three-dimensional structure out of that of a homologous one or the design of new variants. A wide range of features can be used by the researcher for this purpose. The system is written in FORTRAN 77 and E&S GSR functions or the HP implementation of the PHIGS standard, respectively.     

MAXAMIZE. A DNA sequencing strategy advisor.

The MAXAMIZE advisory system determines from user-provided restriction maps an optimal strategy to do nucleotide sequencing by methods involving end-labeled fragments. The maps may be either simple linear restriction maps of fragments or complex circular maps including restriction sites of a vector. The whole system is interactive and is written in the Genetic English language provided by the GENESIS System, a molecular genetics knowledge representation and manipulation package. In addition, MAXAMIZE provides bookkeeping facilities for sequencing and offers advise on how to verify the newly obtained sequence data.     

The MTX package of computer programmes for the comparison of sequences of nucleotides and amino acid residues.

A suite of some dozen programmes written in FORTRAN77 to run on VAX computers using the VMS operating system, and which utilizes a Digital Command Language (DCL) shell to allow it to be menu driven has been in use at the Division of Molecular Biology for about nine months. The package allows the user to obtain both dot matrix and line matrix plots, find and output specific regions of similarity and compute statistics for randomly generated sequences. In all these cases the user may specify either a maximum number of gaps in the match that will be tolerated or a minimum percentage similarity allowable for a match to be registered. The system allows the user to create a batch job for any of these analyses; so, for example, a number of line matrix plots can be specified from a remote alpha-numeric terminal which can be plotted later at a graphics terminal. In addition, computation of quasi-correlation statistics (Qr) for nucleotide sequences or correlation statistics (r) for amino acid residue sequences may be computed. Help facilities and documentation including examples are provided.     

Portable microcomputer software for nucleotide sequence analysis.

The most common types of nucleotide sequence data analyses and handling can be done more conveniently and inexpensively on microcomputers than on large time-sharing systems. We present a package of computer programs for the analysis of DNA and RNA sequence data which overcomes many of the limitations imposed by microcomputers, while offering most of the features of programs commonly available on large computers, including sequence numbering and translation, restriction site and homology searches with dot-matrix plots, nucleotide distribution analysis, and graphic display of data. Most of the programs were written in Standard Pascal (on an Apple II computer) to facilitate portability to other micro-, mini-, and and mainframe computers.     

Computer program for the IBM personal computer which searches for approximate matches to short oligonucleotide sequences in long target DNA sequences.

We describe a program which may be used to find approximate matches to a short predefined DNA sequence in a larger target DNA sequence. The program predicts the usefulness of specific DNA probes and sequencing primers and finds nearly identical sequences that might represent the same regulatory signal. The program is written in the C programming language and will run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running under the MS/DOS and UNIX operating systems. The program has been integrated into an existing software package for the IBM personal computer (see article by Mount and Conrad, this volume). Some examples of its use are given.     

The current status and portability of our sequence handling software.

I describe the current status of our sequence analysis software. The package contains a comprehensive suite of programs for managing large shotgun sequencing projects, a program containing 61 functions for analysing single sequences and a program for comparing pairs of sequences for similarity. The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use. The major interactive programs have 125 pages of online help available from within them. Several new programs are described including screen editing of aligned gel readings for shotgun sequencing projects; a method to highlight errors in aligned gel readings, new methods for searching for putative signals in sequences. We use the programs on a VAX computer but the whole package has been rewritten to make it easy to transport it to other machines. I believe the programs will now run on any machine with a FORTRAN77 compiler and sufficient memory. We are currently putting the programs onto an IBM PC XT/AT and another micro running under UNIX.     

Image analysis of restriction enzyme fingerprint autoradiograms

A genome mapping system has been developed that reads and assemblesdata from clones analysed by restriction enzyme fragmentationand polyacrylamide gel electrophoresis. Input data for the systemcan be most effectively obtained by the use of a scanning densitometerand image-processing package, such as that described in thisarticle. The image-processing procedure involves preliminarylocation of bands, cooperative tracking of lanes by correlationof adjacent bands, a precise densitometric pass, alignment ofthe marker bands with the standard, optional interactive editing,and normalization of the accepted bands. Received on August 31, 1988; accepted on December 6, 1988     

An integrated software system for microcomputer management of recombinant DNA data.

A database-oriented system (pCP123) is described for the manipulation of recombinant DNA data. This system was developed within the context of an integrated software package with spreadsheet, database, graphing and programming capabilities. The system includes two databases, one of sites and another of regions, coordinately handled by a series of macro-programs operated from four user-define menus. A distinctive feature of the system is the possibility of handling both ends of defined functional or structural regions in situations of simulated deletions or insertions.     

A reliable and inexpensive microprocessor system for collection and transfer of raw immunoassay data

A very low cost microprocessor system has been designed to ease data handling problems in a large workload immunoassay laboratory. The microprocessor collects and stores data from many immunoassay detection devices simultaneously, and transfers the data to a minicomputer for analysis as each measurement batch is completed. Stored data are protected against a mains power failure during collection and against non-availability of the minicomputer at transfer time. The system provides fast and reliable transfer of very large amounts of raw data from measurement devices to computer, and therefore facilitates the use of a statistically sound data reduction software package.     

MUCIDS: an operative C environment for acquisition and processing of polarized-light scattered from biological specimens

In this work, we describe a software package, MUCIDS, completelydeveloped in our laboratory, for acquisition and processingof differential polarizxition light-scattering data from specimensof biophysical interest. MUCIDS is a C environment that managesthe whole activity of an instrument used for measurements ofMueller matrix scattering elements. It allows one to capture,analyse, process and display data from this or from other similarlight-scattering experiments. The entire system is suitablefor routine measurements in a general biophysical (or microbiological)laboratory because of its easy handling and maintenance. Thesoftware was written in C lattice and will run on IBM personalcomputers and similar. It uses IBM/DAC and GPIB/IBM interfacecards. Received on October 3, 1989; accepted on March 26, 1990     

PCDRA: PC interactive molecular representation and modeling system

PCDRA was designed to provide the average biologist with a user-friendly molecular display on a low-cost personal computer. The package is menu driven and is built so that a biologist, with tittle or no computing knowledge, finds it easy to use. The system gives a color representation with depth cueing of a protein whose atomic coordinates are stored as a PDB file. Moreover, the system presents several features similar to HYDRA¹ and therefore is a good introduction to molecular graphics, especially for beginners in protein modeling.     

Apple Macintosh programs for nucleic and protein sequence analyses

This paper describes a package of programs for handling and analyzing nucleic acid and protein sequences using the Apple Macintosh microcomputer. There are three important features of these programs: first, because of the now classical Macintosh interface the programs can be easily used by persons with little or no computer experience. Second, it is possible to save all the data, written in an editable scrolling text window or drawn in a graphic window, as files that can be directly used either as word processing documents or as picture documents. Third, sequences can be easily exchanged with any other computer. The package is composed of thirteen programs, written in Pascal programming language.     

Portable file management system in FORTRAN

It has been generally considered that FORTRAN is inferior to MUMPS and other computer languages in its facility to manipulate files and that it is not satisfactorily competent to handle databases. However, it is our finding that FORTRAN is the most widely used language in patient data management systems discussed in recently published papers. Therefore, it now seems appropriate to review and evaluate the validity of this general belief. The objective of this study is to establish a file management system in FORTRAN 77 for use in the construction of a clinical database. Comparative study is conducted on several problems associated with file manipulation, that is, time requirement for file access and access methods for data retrieval.     

Software for genome mapping by fingerprinting techniques

A genome mapping package has been developed for reading andassembling data from clones analysed by restriction enzyme fragmentationand polyacrylamide gel electrophoresis. The package comprises:data entry; matching; assembly; statistical analysis; modelling.Data entry can be either manual or by a semiautomatic systembased on a scanning densitometer. The primary emphasis in theanalytical routines is on flexibility and interactive convenience,so that the operator has full knowledge of and control overthe growing map, but a variety of automatic options are included.The package continually grows to meet the needs of the Caenorhabditisproject. Received on July 17, 1987; accepted on November 20, 1987     

Life cycle assessment through on-line database linked with various enterprise database systems

Goal, Scope and Background  Performing a life cycle assessment (LCA) has been a rather resource and time-consuming business. The method of data collection may be problematic, and the quality of the final results can be influenced by the reliability of the data. Therefore, it is helpful to utilize an on-line data gathering system to save time and to improve the reliability of the collected raw data. Main Features  We have developed an LCA software package for a steel company. The software consists of two major parts: an LCA tool kit and an interface program. The LCA tool kit is a user interface for handling an LCA database server. It has powerful functions to execute systematic analysis, not only for the amount of energy and raw materials, but also for the volume of pollutants generated by each component. The latter is an interface program between a data handling system and an on-line data gathering system. This interface program is linked with three enterprise database systems, such as enterprise resource planning (ERP), an environmental management system (EMS) and an energy server system (ESS). In this study, we compared three different ways of performing LCA. Two of them are on-line methods, and another is manual. Results and Discussion  Among the three methods, the best method was on-line LCA linked with ERP, EMS and ESS. Case studies in steel works have shown that the current method is superior to manual data gathering in terms of time and cost (man-month) savings, data reliability and other applications. Results of life cycle inventory and life cycle impact assessment for steel products have shown monthly fluctuations due to fuel usage ratio, which have not been detected before using manual data gathering. Conclusions  An LCA can be performed quickly, if one is to employ the on-line data gathering system we have developed. The system consists of an LCA software package including the interface program and LCA tool kit, and the enterprise database systems. Case studies for LCA with the on-line system have shown superior performance to that carried out using the manual data entry method. Recommendations and Perspective  This system enables an enterprise to take Type III and conduct benchmarking to other companies or societies within a short time. Also, combining this tool with an environmental performance evaluation or accounting system can allow one to achieve a more progressive environmental management.     

“dendRoAnalyst”: A tool for processing and analysing dendrometer data

Dendrometers are vital tools for studying the response of trees to intra-annual environmental changes in different temporal resolutions, ranging from hourly, daily to weekly time resolution. Dendrometers are increasingly used in forest management and tree physiological studies. Besides the data analysis, data processing is also challenging, time-consuming and potentially error-prone due to the immense number of measurements generated by self-registering electronic dendrometers. We present the package ‘dendRoAnalyst’ based on R statistical software to process and analyse dendrometer data using various approaches. This package offers algorithms for handling and pre-cleaning of dendrometer data before the application of subsequent data analytical steps. This includes identifying and erasing artefacts in dendrometer datasets not related to actual stem circumference change, identifying data gaps within records, and the possibility of change(s) in temporal resolution. Furthermore, the package can calculate different daily statistics of dendrometer data, including the daily amplitude of tree growth. The package dendRoAnalyst is therefore intended to facilitate researchers with a collection of functions for handling and analysing dendrometer data.     

Department of health changes advice on third generation pills

The restriction on the use of third-generation oral contraceptives, pills which contain gestodene and desogestrel, has been lifted, and the pills can now be offered to women who want to use the method. The Committee on Safety of Medicine imposed the 1995 restriction after a study suggested a small increase in the risk of deep vein thrombosis. But after extensive research, the Medicines Commission stated that third generation pills can be prescribed to women provided that they will be informed of the greater risk involved. In addition, third-generation pills would contain new package inserts, explaining the risks of deep vein thrombosis. The warning will state that the risk of deep vein thrombosis in women not taking the pill is 5/100,000 women/year. This risk increases to 15/100,000 women/year in women taking second-generation pills, while it is 25/100,000 women/year in women taking third-generation pills.     

Adopting a database as a solution to managing electron image data

A database was used for data management and interprogram communication in an image processing and three-dimensional reconstruction program suite for biological bundles. The programs were modified from the MRC crystallographic package. The database server works with local and remote programs and data sets, allows simultaneous requests from multiple clients, and maintains multiple databases and data tables within them. It has built-in security for the data access. Several graphical user interfaces are available to view and/or edit data tables. In addition, FORTRAN interface and function libraries are written to communicate with image processing software. The data management overhead is inexpensive, requiring only narrow bandwidth from the network. It easily handles several data tables with over 1000 entries.     

SDSE: A software package to simulate the evolution of a pair of DNA sequences

An algorithm to simulate DNA sequence evolution under a generalstochastic model, including as particular cases all the previouslyused schemes of nucleotide substitution, is described. The simulationis carried out on finite, variable length, DNA sequences througha strict stochastic process, according to the particular substitutionrates imposed by each scheme. Five FORTRAN programs, runningon an IBM PC and compatibles, carry out all the tasks neededfor the simulation. They are menu driven and interfaced to thesystem through a principal menu. All sequence data files usedand generated by the SDSE package conform to the standard GenBankdatabase format, thus allowing the use of any sequence retrievedfrom this databank, as well as the application of other packagesto analyse, manipulate or retrieve simulated sequences. Received on August 23, 1988; accepted on November 15, 1988