Using Situs for the integration of multi-resolution structures

Situs is a modular and widely used software package for the integration of biophysical data across the spatial resolution scales. It has been developed over the last decade with a focus on bridging the resolution gap between atomic structures, coarse-grained models, and volumetric data from low-resolution biophysical origins, such as electron microscopy, tomography, or small-angle scattering. Structural models can be created and refined with various flexible and rigid body docking strategies. The software consists of multiple, stand-alone programs for the format conversion, analysis, visualization, manipulation, and assembly of 3D data sets. The programs have been ported to numerous platforms in both serial and shared memory parallel architectures and can be combined in various ways for specific modeling applications. The modular design facilitates the updating of individual programs and the development of novel application workflows. This review provides an overview of the Situs package as it exists today with an emphasis on functionality and workflows supported by version 2.5.     

Computer simulation of introductory neurophysiology

A computer-assisted learning (CAL) package, NeuroLab, developed for use by first-year university students undertaking professional programs in the health area, is described and evaluated. NeuroLab is a simulation of a laboratory, in which students are able to impale neurons to measure resting membrane potentials and subsequently undertake experiments including measuring resting membrane potentials, determining threshold potentials, measuring refractory periods, and examining effects on membrane potential through altering the membrane permeability to sodium and potassium ions. Students find the package to be a worthwhile learning experience, with 81 +/- 2.2% reporting the package increased their understanding of neuron function, and 78 +/- 2.5% expressing a desire for more CAL packages. Exposure to the package resulted in significantly higher mean scores in a multiple-choice question test on measuring neuron membrane potentials compared with those who were not exposed (mean scores out of 4 of 2.42 and 2.02, respectively, P < 0.001).     

Computer programs for the analysis and the management of DNA sequences.

A program package is described for the management and the analysis of DNA sequence data. The programs - with the exception of a few Fortran routines - are written in the programming language APL. They are best used interactively although batch processing is possible. The package has been in constant use for about 3 years and contains programs for most of the routine problems presently found in a DNA sequencing laboratory.     

FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments

SUMMARY: As was shown in Nagarajan et al. (2005), commonly used approximations for assessing the significance of multiple alignments can be be very inaccurate. To address this, we present here the FAST package, an open-source collection of programs and libraries for efficiently and reliably computing the significance of ungapped local alignments. We also describe other potential applications in Bioinformatics where these programs can be adapted for significance testing. AVAILABILITY: The FAST package includes C++ implementations of various algorithms that can be used as stand-alone programs or as a library of subroutines. The package and a web-server for some of the programs are available at www.cs.cornell.edu/~keich/FAST.     

A collection of programs for nucleic acid and protein analysis, written in FORTRAN 77 for IBM-PC compatible microcomputers.

We have developed a collection of programs for manipulation and analysis of nucleotide and protein sequences. The package was written in Fortran 77 on a Sirius1/Victor microcomputer which can be easily implemented on a large variety of other computers. Some of the programs have already been adapted for use on a Vax 11. Our aim was to develop programs consisting of small, comprehensible and well documented units that have very fast execution times and are comfortably interactive. The package is therefore suitable for individual modifications, even with little understanding of computer languages.     

Analysis and Recognition of Erythroid-Specific Gene Promoters Basing on Degenerate Oligonucleotide Motifs

We developed a method to search for degenerate oligonucleotide motifs specific for certain regions in eukaryotic gene promoters. A procedure of promoter recognition based on these motifs is presented. The methods are integrated within the program package ARGO available for Internet users (http://wwwmgs.bionet.nsc.ru/mgs/programs/argo). This method was applied to study erythroid-specific gene promoters. High efficiency of their recognition is demonstrated.     

Analysis and recognition of promoters for erythroid-specific genes based on degenerative oligonucleotide motifs]

We developed a method to search for degenerate oligonucleotide motifs specific for certain regions in eukaryotic gene promoters. A procedure of promoter recognition based on these motifs is presented. The methods are integrated within program package ARGO available for the Internet users (http://wwwmgs.bionet.nsc.ru/mgs/programs/argo). This method was applied to study erythroid-specific gene promoters. High efficiency of their recognition is demonstrated.     

related: an R package for analysing pairwise relatedness from codominant molecular markers

Analyses of pairwise relatedness represent a key component to addressing many topics in biology. However, such analyses have been limited because most available programs provide a means to estimate relatedness based on only a single estimator, making comparison across estimators difficult. Second, all programs to date have been platform specific, working only on a specific operating system. This has the undesirable outcome of making choice of relatedness estimator limited by operating system preference, rather than being based on scientific rationale. Here, we present a new R package, called related, that can calculate relatedness based on seven estimators, can account for genotyping errors, missing data and inbreeding, and can estimate 95% confidence intervals. Moreover, simulation functions are provided that allow for easy comparison of the performance of different estimators and for analyses of how much resolution to expect from a given data set. Because this package works in R, it is platform independent. Combined, this functionality should allow for more appropriate analyses and interpretation of pairwise relatedness and will also allow for the integration of relatedness data into larger R workflows.     

GONOME: measuring correlations between GO terms and genomic positions

Background

The design of oligonucleotides and PCR primers for studying large genomes is complicated by the redundancy of sequences. The eukaryotic genomes are particularly difficult to study due to abundant repeats. The speed of most existing primer evaluation programs is not sufficient for large-scale experiments.

Results

In order to improve the efficiency and success rate of automatic primer/oligo design, we created a novel method which allows rapid masking of repeats in large sequence files, for example in eukaryotic genomes. It also allows the detection of all alternative binding sites of PCR primers and the prediction of PCR products. The new method was implemented in a collection of efficient programs, the GENOMEMASKER package. The performance of the programs was compared to other similar programs. We also modified the PRIMER3 program, to be able to design primers from lowercase-masked sequences.

Conclusion

The GENOMEMASKER package is able to mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10 000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.     

PCAP: probe choice and analysis package--a set of programs to aid in choosing synthetic oligomers for contig mapping

In the program, PCAP, we provide a methodology for choosingsynthetic oligonucleotide probes to be used in contig mappingexperiments. The package serves the purpose of presenting aseries of short oligonucleotides (8–12mers) that are chosenbased on constraints with respect to frequency of occurrencewithin a particular genome and the G+C content of the oligonucleotides.The four programs contained within the package: (i) convertGenBank files to a format useable by the package; (ii) calculatetrinucleotide and tetranucleotide frequencies in available sequencedata on a particular species; (iv) present the user with upperand lower bounds on the frequencies of hybridization sites foroligonucleotide probes of length 8–12, (iv) allow theuser to place constraints on site frequency and G+C contentand provides a list of short probe sequences that fit thesecriteria. These sequences can then be synthetically producedand used in hybridization experiments to carry out contig mapping.     

matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements

SUMMARY: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation of data packages for curating, distributing and working with probe sequence data in a uniform, across-types-of-microarrays manner. While the implementation is specific to the Bioconductor project, the ideas and general strategies are more general and could be easily adopted by other projects. AVAILABILITY: The R package matchprobes is available under LGPL at http://www.bioconductor.org SUPPLEMENTARY INFORMATION: The package contains documentation in the form of a vignette and manual pages.     

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.     

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.     

The computer program package "SAMSON" for analysis of primary structure of biopolymers

A program package "SAMSON" for the computer analysis of biopolymer primary structures is described. All possible modes of sequence investigation are considered. The programs for sequence comparison are described in some details. The general principles of a program package organisation and of its user interface are also mentioned. For more complete information see Vernoslov S.E. et al. "Program package "SAMSON" for the analysis of the polymer primary structures", parts 1 and 2, Poustchino, ONTI NCBI, 1989.     

A convenient and adaptable microcomputer environment for DNA and protein sequence manipulation and analysis.

We describe the further development of a widely used package of DNA and protein sequence analysis programs for microcomputers (1,2,3). The package now provides a screen oriented user interface, and an enhanced working environment with powerful formatting, disk access, and memory management tools. The new GenBank floppy disk database is supported transparently to the user and a similar version of the NBRF protein database is provided. The programs can use sequence file annotation to automatically annotate printouts and translate or extract specified regions from sequences by name. The sequence comparison programs can now perform a 5000 X 5000 bp analysis in 12 minutes on an IBM PC. A program to locate potential protein coding regions in nucleic acids, a digitizer interface, and other additions are also described.     

NEUREC - a program package for 3D-reconstruction from serial sections using a microcomputer

A software package is described to reconstruct three-dimensional pictures in true perspective from a series of parallel sections using a low-cost computer system (Apple II plus). Data sampling via a graphic tablet and graphical output on the monitor screen or a digital plotter are assigned to different programs under control of a menu program. The number of data representing the object under study is unlimited. Originally written in BASIC, the programs were translated to machine language. As an application of the package, reconstructions of an identified large interneuron of the locust brain are presented.     

QuantWorm: A Comprehensive Software Package for Caenorhabditis elegans Phenotypic Assays

Phenotypic assays are crucial in genetics; however, traditional methods that rely on human observation are unsuitable for quantitative, large-scale experiments. Furthermore, there is an increasing need for comprehensive analyses of multiple phenotypes to provide multidimensional information. Here we developed an automated, high-throughput computer imaging system for quantifying multiple Caenorhabditis elegans phenotypes. Our imaging system is composed of a microscope equipped with a digital camera and a motorized stage connected to a computer running the QuantWorm software package. Currently, the software package contains one data acquisition module and four image analysis programs: WormLifespan, WormLocomotion, WormLength, and WormEgg. The data acquisition module collects images and videos. The WormLifespan software counts the number of moving worms by using two time-lapse images; the WormLocomotion software computes the velocity of moving worms; the WormLength software measures worm body size; and the WormEgg software counts the number of eggs. To evaluate the performance of our software, we compared the results of our software with manual measurements. We then demonstrated the application of the QuantWorm software in a drug assay and a genetic assay. Overall, the QuantWorm software provided accurate measurements at a high speed. Software source code, executable programs, and sample images are available at www.quantworm.org. Our software package has several advantages over current imaging systems for C. elegans. It is an all-in-one package for quantifying multiple phenotypes. The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. It can be run on multiple platforms and easily customized to cope with new methods and requirements.     

DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

The components of complex peptide mixtures can be separated by liquid chromatography, fragmented by tandem mass spectrometry, and identified by the SEQUEST algorithm. Inferring a mixture's source proteins requires that the identified peptides be reassociated. This process becomes more challenging as the number of peptides increases. DTASelect, a new software package, assembles SEQUEST identifications and highlights the most significant matches. The accompanying Contrast tool compares DTASelect results from multiple experiments. The two programs improve the speed and precision of proteomic data analysis.