A microcomputer program and fast analog to digital converter card for the analysis of fluorescence induction transients

A microcomputer program and an analog to digital conversion card were developed for the analysis of fluorescence induction curves. The program and the analog to digital conversion card are compatible with all commercially available fluorometers. Most of the current analysis methods for fluorescence induction curves are implemented in the program, including analysis of OIDPSMT-kinetics, dissection of fluorescence quenching into two components, measurement of the slope of the fluorescence curve, complementary area analysis and analysis of energy spillover from PS II to PS I. The program can also do basic statistical calculations from the measured parameters. The architecture of the program is open, allowing the user to add new methods to the main body of the program. Split time-scale is used in data capture and analysis. A new procedure facilitates accurate determination of F₀.     

Sequence determination of oligosaccharides and regular polysaccharides using NMR spectroscopy and a novel Web-based version of the computer program CASPER

A WWW-interface to a program for structure elucidation of oligo- and polysaccharides using NMR data, CASPER, is presented. The interface and the underlying program have been extensively tested using published data and it was able to simulate 13C NMR spectra of >200 structures with an average error of about 0.3 ppm/resonance. When applied to the repeating units of Escherichia coli O-antigens the published structures were found among the five highest ranked structures in 75% of the cases. The average deviation between calculated and experimental 13C chemical shifts was 0.45 ppm. Oligosaccharide spectra were calculated with even better accuracy (0.23 ppm/resonance) and the correct structure was ranked 1st or 2nd in all the cases examined. Additional NMR experiments that may be required to distinguish between candidate structures are aided by the assignments provided by the program. This computational approach is also suitable for use in structural confirmation of chemically or enzymatically synthesized oligosaccharides. The program is found at http://www.casper.organ.su.se/casper.     

NMπ—improved re‐implementation of NM+, a software for estimating gene dispersal and mating patterns

This study introduces the NMπ computer program designed for estimation of plant mating system and seed and pollen dispersal kernels. NMπ is a re‐implementation of the NM+ program and provides new features such as support for multicore processors, explicit treatment of dioecy, the possibility of incorporating uniparentally cytoplasmic markers, the possibility of assessing assortative mating due to phenotypic similarity and inference about offspring genealogies. The probability model of parentage (the neighbourhood model) accounts for missing data and genotyping errors, which can be estimated along with regular parameters of the mating system. The program has virtually no restrictions with respect to a number of individuals, markers or phenotypic characters. A console version of NMπ can be run under a wide variety of operating systems, including Windows, Linux or Mac OS. For Windows users, a graphical user interface is provided to facilitate operating the software. The program, user manual and example data are available on http://www.ukw.edu.pl/pracownicy/plik/igor_chybicki/3694/ .     

LINKER: a program to generate linker sequences for fusion proteins

The construction of functional fusion proteins often requires a linker sequence that adopts an extended conformation to allow for maximal flexibility. Linker sequences are generally selected based on intuition. Without a reliable selection criterion, the design of such linkers is often difficult, particularly in situations where longer linker sequences are required. Here we describe a program called LINKER which can automatically generate a set of linker sequences that are known to adopt extended conformations as determined by X-ray crystallography and NMR. The only required input to the program is the desired linker sequence length. The program is specifically designed to assist in fusion protein construction. A number of optional input parameters have been incorporated so that users are able to enhance sequence selection based on specific applications. The program output simply contains a set of sequences with a specified length. This program should be a useful tool in both the biotechnology industry and biomedical research. It can be accessed through the Web page http://www.fccc. edu/research/labs/feng/linker.html.     

A simulation program examining the use of ratios as raw variables in analyses of variance

An interactive, BASIC-PLUS, simulation program is described for performing a large number of multivariate analyses in accord with, or in violation of, known underlying models. Using a PDP 11/40 computer, random numbers are generated and converted into bivariate normal observations X and Y. These data are then analyzed according to three models. The three analyses are: (1) a standard analysis of variance ignoring the concomitant variable; (2) an analysis of covariance; (3) an analysis of variance on the ratio Y/X. The program can be used to examine the effect of performing multivariate analyses on data transformed into ratios. The utility of the program is the simplicity with which one can alter the underlying models and/or the mathematical relationships between X and Y. Output provides comparisons between models by accumulating rejections and other statistics on critical F-values for each model.     

Redasoft Plasmid 1.1: software for easy, efficient cloning and map drawing

A computer program is described which creates circular and linear genetic maps with or without sequences, performs restriction analysis, and simulates basic molecular cloning operations. Redasoft Plasmid 1.1 is a user-friendly program for Windows 95/98/NT/2000, designed to generate high quality genetic maps for presentation and publication and to aid the molecular biologist in selecting restriction endonucleases for common molecular cloning experiments. The program incorporates an integrated web browser and can automatically generate complete, labeled maps from sequences on the Internet.     

SChiSM2: creating interactive web page annotations of molecular structure models using Jmol

SChiSM2 is a web server-based program for creating web pages that include interactive molecular graphics using the freely-available applet, Jmol, for illustration. The program works with Internet Explorer and Firefox on Windows, Safari and Firefox on Mac OSX and Firefox on Linux. Availability: The program can be accessed at the following address: http://ci.vbi.vt.edu/cammer/schism2.html.     

Community based rehabilitation program for people with musculoskeletal conditions

Community based rehabilitation program in people with musculoskeletal conditions was evaluated using Dartmouth COOP Functional Health Assessment Charts/WONCA (COOP/WONCA charts). The program consisted of educative and training protocol in a primary healthcare setting. It had two parts, both with six visits, in the first part three times a week and in the second part once a week. Clients with musculoskeletal conditions (N = 204) were included if they agreed to take active part in the rehabilitation process. The first part of the program was completed by 77 clients, and complete program by 52 subjects. Positive changes on the COOP/WONCA charts were achieved by more than 50% of the subjects that completed the program, in all categories but Social Activities. The program proved effective in terms of short-term evaluation with COOP/WONCA charts in those that complete the program. The high dropout rate and long-term efficiency have yet to be investigated.     

GCI: A network server for interactive 3D graphics

The Graphics Command Interpreter (GCI) is an independent server module that can be interfaced to any program that needs interactive three-dimensional (3D) graphics capabilities. The principal advantage of GCI is its simplicity. Only a limited set of powerful features have been implemented, including object management, global and local transformations, rotation, translation, clipping, scaling, viewport operations, window management, menu handling and picking.GCI and the master (client) program it serves run concurrently, communicating over a local or remote TCP/IP network. GCI sets up socket communication and provides a 3D graphics window and a terminal emulator for the master program. Communication between the two programs is via ASCII strings over standard I/O channels. The implied language for messages is very simple. GCI interprets messages from the master program and implements them as changes of graphical objects or as text messages to the user. GCI provides the user with facilities to manipulate the view of the displayed 3D objects interactively, independently of the master program, and to communicate mouse-controlled selection of menu items or 3D points as well as keyboard strings to the master program.The program is written in C and initially implemented using the Silicon Graphics GL graphics library. As the need to link special libraries to the master program is completely avoided, GCI can very easily be interfaced to existing programs written in any language and running on any operating system capable of TCP/IP communication. The program is freely available.     

Delay and characteristics of scorpion bite management in the Sidi-Bouzid region

Scorpion envenomation represents a potential danger in the 2/3 of Tunisia's territory but Sidi Bouzid area is the most infected with 1/6 of the piqued in Tunisia. The purpose of the study was to assess the result of a program for scorpion control in Sidi Bouzid and especially the delay from being stung to access to health care service. The analysis of data related to program shows that the delay was decreased only in 4 districts out of 11. This situation should be explained by such factors as information and behaviour of population, access to health care.... It is necessary to increase the action recommended by the program and to behold specific characteristics of each district.     

ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors

ClusterDraw is a program aimed to identification of binding sites and binding-site clusters. Major difference of the ClusterDraw from existing tools is its ability to scan a wide range of parameter values and weigh statistical significance of all possible clusters, smaller than a selected size. The program produces graphs along with decorated FASTA files. ClusterDraw web server is available at the following URL: http://flydev.berkeley.edu/cgi-bin/cld/submit.cgi     

The program Proteocat as a tool for planning of proteomic experiments

ProteoCat is a computer program that has been designed to help researchers in the planning of large-scale proteomic experiments. The central part of this program is the unit of hydrolysis simulation that supports 4 proteases (trypsin, lysine C, endoproteinases Asp-N and GluC). For peptides obtained after virtual hydrolysis or loaded from data files a number of properties important in mass-spectrometric experiments can be calculated and predicted; the resultant data can be analyzed or filtered (to reduce a set of peptides). The program is using new and improved modifications of own earlier developed methods for pI prediction, which can be also predicted by means of popular pKa scales proposed by other reseachers. The algorithm for prediction of peptide retention time has been realized similarly to the algorithm used in the SSRCalc program. Using ProteoCat it is possible to estimate the coverage of amino acid sequences of analyzed proteins under defined limitation on peptides detection, as well as the possibility of assembly of peptide fragments with user-defined minimal sizes of “sticky” ends. The program has a graphical user interface, written on JAVA and available at http://www.ibmc.msk.ru/LPCIT/ProteoCat.     

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 TEFOOL12 is to provide people interested in drugdesign with an easy-to-handle program where some of the mostimportant techniques in QSAR are included. The program permitsthe selection of the training series, performs regression calculationsand searches for optimum substituents. The latter is achievedby using either a Hansch's strategy or geometrical procedures.The program is interactive and can be implemented on an IBM-PCor compatible microcomputer. Although TEFOOL/2 has been developedfor its application in drug design studies, its great flexibilitymakes it suitable for application to any experimental designor optimization process. Received on November 22, 1988; accepted on March 21, 1989     

Multi-query sequence BLAST output examination with MuSeqBox

SUMMARY: MuSeqBox is a program to parse BLAST output and store attributes of BLAST hits in tabular form. The user can apply a number of selection criteria to filter out hits with particular attributes. MuSeqBox provides a powerful annotation tool for large sets of query sequences that are simultaneously compared against a database with any of the standard stand-alone or network-client BLAST programs. We discuss such application to the problem of annotation and analysis of EST collections. AVAILABILITY: The program was written in standard C++ and is freely available to noncommercial users by request from the authors. The program is also available over the web at http://bioinformatics.iastate.edu/bioinformatics2go/mb/MuSeqBox.html.     

NKCELPRO: a program for microcomputer applicable to the study of responses of spontaneous cytotoxicity

A microcomputer program (NKCELPRO) which expedites the exact quantification of various parameters referring to NK cell activities is described. The program is written in BASIC language and computes the activities of cell-mediated cytotoxicity by collating and reducing radioactive count data obtained from 51Cr releasing assays. The information generated by this program includes statistics such as the average values, fitting by last square regression line with its correlation coefficient, as well as determination of the percent specific lysis and lytic units/10(7) effector cells according to any reference value previously defined by the operator. Special program features allow for a certain flexibility in the experimental protocol design as well as in the graphic expression of the results. Data storage on a disk with filing purposes for subsequent studies is also available.     

A microcomupter program for the computation of free energy of the secondary structure of RNA oligomers by Ninio's rules

An interactive microcomputer program for the rapid computation of the free (ΔG) of the secondary structure of RNA molecules is presented. The program assigns free energies (in kcal/mol) to helices; bulge, internal, and multi-branch loops; hairpins; unparied, and G:C termini according to Ninio's rules, and displays a running total during computation. It is written in ‘Microsoft Basic’ and is apllicable to virtually any Basic system with no modification. The program enables rapid bench-top determinations of free energies attributable to secondary structure features of RNA oligomers, and eliminates both the tedium and risk of error associated with manual calculations.     

ANGSD: Analysis of Next Generation Sequencing Data

Background

High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously.

Results

We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods.

Conclusions

The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd. The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0356-4) contains supplementary material, which is available to authorized users.     

gff2aplot: Plotting sequence comparisons

SUMMARY: gff2aplot is a program to visualize the alignment of two sequences together with their annotations. Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis. AVAILABILITY: gff2aplot is freely available under the GNU software licence and can be downloaded from the address specified below. Supplementary information: http://genome.imim.es/software/gfftools/GFF2APLOT.html     

Computer-assisted assignment of peptides with non-standard amino acids

Summary A comprehensive peptide assignment program and its application to a cyclic peptide, cyclosporin A, are presented in this paper. A group of graph theoretical algorithms using fuzzy logic are discussed with the aid of examples from cyclosporin A. The algorithms deal with heavily overlapped peaks, recover disjointed and distorted spin coupling networks, and include strategies for sequence-specific assignment. A procedure to extend the Protein Knowledge Base for automatically assigning non-standard amino acid residues is also presented. The program is capable of completely automated assignment for small peptides (20 residues). For such molecules, it is insensitive to whether the peptide chain is cyclic or acyclic, and to whether amide protons are present or absent. For larger peptides/proteins, more user interaction is required and the sequence-specific assignment step usually must proceed through fragments smaller than the full length to avoid problems due to occurrence of a combinatorial explosion. The program can be applied as a rigorous tool to check manual assignments. The fuzzy graph theoretical concepts built in the program are illustrated with 2D proton spectra of a peptide, but may be extended to higher-dimensional spectra, other biopolymers, natural products and other organic structures.