Automatic identification of structural gene fragments using a set of peptides

A computer program is designed to facilitate the identification of coding gene's fragments using a set of peptides. The program is written on Basic programming language for personal computer "Iskra-226" (USSR). To accelerate some operations, computer code commands are used. Treatment of 50 DNA fragments by means of 10 peptides takes ca. 1 h of computer time. The program outputs list coding gene's fragments and corresponding peptides. The suggested algorithm is based on our finding that the number of false identifications of a coding gene fragments may be predicted by Poisson distribution and minimized using correct criteria. The suggested method enables one to evaluate the reliability of the true identification of DNA fragments in case of mistakes in primary structure of the gene fragments or peptides.     

jMHC: software assistant for multilocus genotyping of gene families using next-generation amplicon sequencing

Genotyping of multilocus gene families, such as the major histocompatibility complex (MHC), may be challenging because of problems with assigning alleles to loci and copy number variation among individuals. Simultaneous amplification and genotyping of multiple loci may be necessary, and in such cases, next-generation deep amplicon sequencing offers a great promise as a genotyping method of choice. Here, we describe jMHC, a computer program developed for analysing and assisting in the visualization of deep amplicon sequencing data. Software operates on FASTA files; therefore, output from any sequencing technology may be used. jMHC was designed specifically for MHC studies but it may be useful for analysing amplicons derived from other multigene families or for genotyping other polymorphic systems. The program is written in Java with user-friendly graphical interface (GUI) and can be run on Microsoft Windows, Linux OS and Mac OS.     

A nonlinear regression program for small computers

A BASIC computer program for performing weighted nonlinear regression is described and a listing of the program is given. The program, which is small and simple to use, has been designed to be run by users with little knowledge of mathematics or computers. Robust methods of analysis are described which may be applied to data in which experimental errors are not normally distributed, and the program incorporates one such method. It is shown that the program is useful for the analysis of data conforming to the Michaelis-Menten equation, a single exponential, and to binding equations, and other applications are discussed.     

The SEQANAL and SEQTALK programs: a new method of access to high-resolution nucleotide sequence comparison and analysis programs from a remote laboratory mini- or microcomputer

A new method of access has been devised for biologists requiringthe use of computer programs offering high-resolution analysisand comparison of nucleotide sequence data. The strategy involvesthe development of a pair of computer programs, called SEQANALand SEQTALK, designed to operate in tandem. SEQANAL is a largeand complex program intended to be used to discover regionsof internal repeats and dyad symmetries within one sequence,or regions of homology, complementarity or optimal alignmentbetween two sequences. Three algorithms are supported: thoseof Staden (1977, 1978); of Korn et al. (1977); Queen and Korn(1980); and the newly-described exhaustive tree-searching algorithmof Burnett et al. (1985, 1986). The SEQTALK program is a small,portable, interactive, frontend program with which the usercan specify the instructions to control the SEQANAL program.Together, the SEQANAL and SEQTALK programs permit analyses tobe performed at a remote facility on a mainframe computer underthe complete control of a distant user equipped with minimalcomputing facilities, and without needing networking facilities. Received on May 23, 1985; accepted on August 13, 1985     

Focus on the patentability of computer programs

The Nuts and Bolts section of our Journal (mirrored on the ICCNS society web site), is meant to provide a very practical way to share useful information, that goes beyond the scope of cell signaling and basic CCN protein biology. Considering the number of requests we have had for information related to protection of Intellectual Property (IP), I am pleased to initiate what will be a series of articles that will focus on various IP topics. The inaugural topic is the protection of computer programs. Some colleagues may wonder how and why the patentability of computer programs is a topic of interest for scientists working on CCN proteins . . . As a matter of fact, to assist us in analyzing the potential involvement of CCN3 in human genetic diseases, we considered developing a computer program designed to analyze large amounts of data. Sharing the concepts and the computer program raised concerns regarding IP and protection of the software that we would handle. We believe that many colleagues have encountered similar problems. This article provides a short focus on computer program patentability. It is aimed to provide basic legal information, and to help our readers in understanding the process. It is not intended to replace IP counselors or technology transfer departments. Future articles will address other practical aspects of IP protection.     

PC-based system for an objective quantification of manual movement disability for clinical and scientific purposes

In clinical management and research of movement disorders exact knowledge about the extent of motor impairment is essential. This paper presents a computer program which allows for an objective measurement of manual movement disability. The program was developed for standard hardware and can easily be used in a variety of clinical and research environments. The program runs on MS-DOS computers and uses a Microsoft computer mouse as the only input device. The temporal resolution is 100 Hz, the spatial resolution 400 dots per inch. The user may choose between standard test sets or he may design sets according to his individual needs from a pool of available protocols which includes tracking tasks, ballistic tasks, complex sequential tasks, and finger tapping. All tasks are implemented in a similar way in order to keep the test environment as consistent as possible for the patient. The patient must usually carry out movements which correspond to the movements of a target symbol on the computer screen. This entails the manipulation of a follower symbol, also visible on the computer screen, via the computer mouse. The program itself and the theoretical background of the protocols are described in the paper. Additionally, preliminary results from pilot experiments are presented.     

综合分离分析的微机程序设计及其应用

基于单基因遗传模型,我们在IBM PC/XT微型计算机上,用BASIC语言设计了综合分离分析程序。并应用该计算机程序分析了133个用家族法和家族史法调查的寻常性鱼鳞癣核心家系,98个仅用家族法调查的寻常性鱼鳞癣核心家系和101个原因不明的父母表型正常的感音神经性耳聋核心家系。结果表明,该计算机程序可用于遗传方式分析和遗传咨询。     

MOL3D,a modular and interactive program for molecular modeling and conformational analysis: I — basic modules

MOL3D is a generalized machine-independent computer program that lets the user interactively build 3D structures with different display options, such as wire, ball-and-stick and CPK representations. The program, which uses its own graphics package and driver, is designed to be very user friendly through the use of commands and menus. It has powerful transformation capabilities, such as software rotations, superpositions and zooming, and it is equipped with a fragment database that allows the user to build complex structures. The algorithm presented here is designed to perform computations in all the conformational space and therefore can be used to predict experimentally available quantities, such as NMR coupling constants. The program is efficient in the sense that it handles only dihedral angles in the first steps; as a result, it allows a rapid sampling of a great number of points through the entire conformational space. The user can choose between grid and Monte-Carlo searches of energy minimization, using a reasonable amount of computer time.     

Spreadsheet-based program for alignment of overlapping DNA sequences.

Molecular biology laboratories frequently face the challenge of aligning small overlapping DNA sequences derived from a long DNA segment. Here, we present a short program that can be used to adapt Excel spreadsheets as a tool for aligning DNA sequences, regardless of their orientation. The program runs on any Windows or Macintosh operating system computer with Excel 97 or Excel 98. The program is available for use as an Excel file, which can be downloaded from the BioTechniques Web site. Upon execution, the program opens a specially designed customized workbook and is capable of identifying overlapping regions between two sequence fragments and displaying the sequence alignment. It also performs a number of specialized functions such as recognition of restriction enzyme cutting sites and CpG island mapping without costly specialized software.     

A Monte Carlo program for photon transport using analogue sampling of scattering angle in coherent and incoherent scattering processes

A computer program was developed for the Monte Carlo simulation of photon transport. The program was designed for photon transport simulation in geometries occurring in diagnostic radiology and especially for the investigation of scattered radiation. A method is described for the analogue sampling of scattering angle in coherent and incoherent scattering processes. The two scattering processes are treated separately, and the influence of coherent scattering, an often neglected process, can be estimated quantitatively. The program can also be used for the calculation of the energy imparted to water slabs and fluorescent screens.     

A generalized system for automation of enzyme assays

A flow system was developed, using a Technicon AutoAnalyzer, that is readily adaptable to a range of enzyme assays. The system includes lines for pumping substrate, cofactor, buffer and enzyme and for generating linear gradients. By using a variable-speed proportioning pump the incubation time may be continuously varied, and the system also allows for continuous variation in the pH, substrate or cofactor concentration, incubation temperature and enzyme concentration. A FORTRAN V program was written that uses instrument calibrations to calculate the flow rates in the individual lines, the incubation time and the characteristics of the gradient used. The computer then prints out instructions for preparation of reagents to give a required reaction mixture, weighing sheets for stock solutions and the results of the assay in international units in suitable tables and graphs. The flow system and computer program are designed to facilitate the automation of manual assays. A detailed example is given of the use of the system [the assay of three dehydrogenases in yeast: l(+)-lactate dehydrogenase, d(-)-lactate dehydrogenase and succinate dehydrogenase], and the general applications of the method are discussed. The program has been deposited as Supplementary Publication no. SUP 50002 at the National Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms indicated in Biochem. J. (1970), 116, 7.     

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.     

用于质量性状通径分析微机程序设计及其应用

基于质量性状通径分析模型,我们在IBM PC/XT微型计算机上,用BASIC语言设计了通径分析程序PATH。并用该程序分析了315个原因不明精神发育迟滞(MR)的核心家系。分析结果表明,轻度、中度和重度MR的遗传度分别为0.79、0.88和0.90。仅在轻度MR中发现有教养传递作用。该程序可用于教养和生物遗传分析。     

A new test for linkage in the presence of locus heterogeneity.

The detection of linkage in complex traits, although potentially of the greatest value, has proved very difficult. One reason may be the drastic effect that locus heterogeneity has on statistical power. We propose a new test for linkage in the presence of heterogeneity, based upon the sum of individual pedigree maximum lod scores, combined with a bootstrap method for estimating the null-hypothesis distribution. The technique is designed to exploit modern computer capability and to avoid reliance on asymptotic-distribution theory. Numerical comparisons indicate that for small pedigrees this new test can detect linkage with 30%-50% less data than are required by standard methods. A computer program for simulating the distribution and for performing the test of linkage is available from the authors.     

On-line computer processing of pressure data from cardiac catheterizations.

A flexible program system for on-line analysis of pressure data from cardiac catheterizations is described. The programs are implemented on an IBM 1800 computer, equipped with remote oscilloscope/keyboard terminals. The current computer system can handle any combination of up to 4 pressure signals. During catheterization, measurement specifications (i.e. calibration levels or sites of pressure recordings) are entered via the keyboard immediately before each recording. As an option the whole expected measurement sequence may be stored on disk before the catheterization starts. This method will minimize the necessary interaction with the computer when the same catheterization procedure is used on several occasions. Changes from the predetermined scheme may, however, be undertaken before each recording to meet with unexpected events that may arise during the catheterization. After computer detection of calibration levels, the recorded signals are digitized during 20 seconds and analysed beat-by-beat. Calculated values are averaged and presented on the terminal oscilloscope in tabular and/or graphic form. The waveform analysis performed by the program system is validated in a statistical comparison between manually and automatically computed values.     

Use of computer simulations in microbial and molecular genetics

The development of five computer programs in microbial and molecular genetics is described. Four of these are simulations of genetic and physical mapping experiments, designed to give students experience in generating and analysing meaningful data, and to help in the consolidation of the concepts underlying the simulation. They should be used after the experiment proper has been performed, rather than as a substitute for it. The fifth is an interactive learning program on the genetic coding mechanism.     

DIODA: delineation and feature extraction of microscopical objects.

A computer program is described for delineation and measurement of microscopical objects, such as cells and chromosomes, which may have been scanned using absorbance, fluorescence or reflectance microscopy. The quality of the object delineation is optimized through the controur ratio, which is simply computed from the object contour. Geometrical features, like the perimeter and area are computed. A new definition is introduced for the background region, especially suited for the analysis of closely packed objects. This definition is based upon a comparison between total staining material content values resulting from a variety of methods and circumstances. The program is principally intended for use in the on-line real-time environment of a small laboratory computer, but may be used off-line as well. It has facilities for displaying the results and the process by which they are produced. A program module is described for displaying scan data on a bilevel display using an adaptation of the sigma-delta method.     

The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure

One of the primary goals of population genetics is to succinctly describe genetic relationships among populations, and the computer program STRUCTURE is one of the most frequently used tools for doing so. The mathematical model used by STRUCTURE was designed to sort individuals into Hardy–Weinberg populations, but the program is also frequently used to group individuals from a large number of populations into a small number of clusters that are supposed to represent the main genetic divisions within species. In this study, I used computer simulations to examine how well STRUCTURE accomplishes this latter task. Simulations of populations that had a simple hierarchical history of fragmentation showed that when there were relatively long divergence times within evolutionary lineages, the clusters created by STRUCTURE were frequently not consistent with the evolutionary history of the populations. These difficulties can be attributed to forcing STRUCTURE to place individuals into too few clusters. Simulations also showed that the clusters produced by STRUCTURE can be strongly influenced by variation in sample size. In some circumstances, STRUCTURE simply put all of the individuals from the largest sample in the same cluster. A reanalysis of human population structure suggests that the problems I identified with STRUCTURE in simulations may have obscured relationships among human populations—particularly genetic similarity between Europeans and some African populations.     

BP: A microcomputer program for use in a hypertension clinic

This paper presents details of a computer program, BP, designed for use with an outpatient clinic. The program is implemented on a PET4000, microcomputer and is intended principally for a hypertension follow-up clinic, although it could be easily adapted for other clinics. It allows for initial patient data entry, the entry of data acquired at subsequent visits, the alteration of data, list of all data or a pre-determined subset, and a data sort and tabulation facility. The program is intended to be run by staff who have little experience with computers.