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PubMed1996

MTT: a software tool for quality control in sequence assembly.

A large-scale sequencing project requires a tool to control the quality of the input data because a sizable number of trace data may be of low quality. If these data are allowed to enter the sequence assembly pipeline, harm will be done. Hence, it is important to detect such data as soon as possible. MTT (Move-Track-Trim) is a software package analyzing the quality of the lanes. It subjects each lane to a series of tests, and if a lane does not pass all tests, it is flagged as a "bad" lane. The use has a chance to examine both the "good" and the "bad" lanes and reclassify a "bad" lane as "good," or vice versa. Alternatively, the user may decide to retrack the gel or get rid of some lanes altogether. As a by-product of the analysis, MTT performs other useful functions. It trims the lanes and compresses the lane files and moves them to the directories where assembly is carried out. It also generates some useful statistics describing the quality of the gel.

Base Sequence↗

PubMed2004

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

Databases, Genetic↗

PubMed2005

WinPop 2.5: software for representing population genetics phenomena.

The curriculum for genetics courses is shifting from a classical to a more molecular genetics focus, increasing the importance of subjects such as population genetics. Population genetics is a computational and statistical field that requires a good understanding of the nature of stochastic events. It is a difficult field for biology students with a limited mathematical background and there is a need for visualisation tools to facilitate understanding by the use of practical examples. WinPop provides students and researchers with a visual tool to allow the simulation and representation of population genetics phenomena. WinPop is a user-friendly software meant for use in population genetics courses and basic research. WinPop 2.5 contains six different modules that represent and simulate population genetics models. Genotype and allele frequencies are calculated under the different models: panmixia, genetic drift, assortative matings, selection, gene flow and mutation. The program's interface presents information in Cartesian graphics and isosceles triangular coordinate systems, allowing the user to save graphical and textual data output from the simulations. WinPop is developed in Visual Basic 6.0 and uses Windows 95 and higher. WinPop 2.5 can be downloaded from http://www.genedrift.org/winpop.php.

Algorithms↗

PubMed1995

TRAMP: a software package for generating transposon maps.

TRAMP is a software package for generating transposon maps that are used for DNA sequencing. The package provides a variety of automated tools that can always be overridden by the user. The central part of the package is its selection algorithm that finds the most robust map with the smallest number of inserts. TRAMP has been in daily use by the sequencing team at LBL since it was introduced in the Spring of 1994. It is applicable to any sequencing project utilizing the directed strategy.

Algorithms↗

PubMed1995

NUVIEW: software for display and interactive manipulation of nucleic acid models.

The NUVIEW software package allows skeletal models of any double helical nucleic acid molecule to be displayed on a graphics monitor and to apply various rotations, translations and scaling transformations interactively, through the keyboard. The skeletal model is generated by connecting any pair of representative points, one from each of the bases in the basepair. In addition to the above mentioned manipulations, the base residues can be identified by using a locator and the distance between any pair of residues can be obtained. A sequence based color coded display allows easy identification of sequence repeats, such as runs of Adenines. The real time interactive manipulation of such skeletal models for large DNA/RNA double helices, can be used to trace the path of the nucleic acid chain in three dimensions and hence get a better idea of its topology, location of linear or curved regions, distances between far off regions in the sequence etc. A physical picture of these features will assist in understanding the relationship between base sequence, structure and biological function in nucleic acids.

Animals↗

PubMed1996

GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space.

GEOMETRY is a software package for the analysis of nucleotide sequences using the method of statistical geometry in sequence space. The package consists of programs performing estimation of the average geometry of sequence quartets, analysis of positional variability and computer simulation of parallel and tree-like sequence divergence with user-defined parameters. It provides an independent tool for evaluation of the reliability of conventional phylogenetic trees and calibration of the time of sequence divergence. GEOMETRY may be of interest for all scientists engaged in the study of molecular phylogeny. The package is available by anonymous FTP from ftp.bionet.nsk.su, directory /incoming/molevol/geom.exe, and will be available from EMBL file server (URL: http://@www.ebi.ac.uk)

Algorithms↗

PubMed1997

Software for DNA sequencing by hybridization.

Sequencing by hybridization (SBH) is a promising alternative approach to DNA sequencing and mutation detection. Analysis of the resolving power of SBH involves rather difficult combinatorial and probabilistic problems, and sometimes computer simulation is the only way to estimate the parameters and limitations of SBH experiments. This paper describes a software package, DNA-SPECTRUM, which allows one to analyze the resolving power and parameters of SBH. We also introduce the technique for visualizing multiple SBH reconstructions and describe applications of DNA-SPECTRUM to estimate various SBH parameters. DNA-SPECTRUM is available at http://www-hto.usc.edu/software/sbh/index. html.

Base Sequence↗

PubMed2000

PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance.

MOTIVATION: The identification of sequence patterns involved in gene regulation and expression is a major challenge in molecular biology. In this paper we describe a novel algorithm and the software for searching nucleotide and protein sequences for complex nucleotide patterns including potential secondary structure elements, also allowing for mismatches/mispairings below a user-fixed threshold, and assessing the statistical significance of their occurrence through a Markov chain simulation. RESULTS: The application of the proposed algorithm allowed the identification of some functional elements, such as the Iron Responsive Element, the Histone stem-loop structure and the Selenocysteine Insertion Sequence, located in the mRNA untranslated regions of post-transcriptionally regulated genes with the assessment of sensitivity and selectivity of the searching method. AVAILABILITY: A Web interface is available at: http://bigarea.area.ba.cnr.it:8000/EmbIT/Pats earch.html.

3' Untranslated Regions↗

PubMed2001

MEGA2: molecular evolutionary genetics analysis software.

UNLABELLED: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. AVAILABILITY: http://www.megasoftware.net. CONTACT: s.kumar@asu.edu

DNA↗

PubMed1986

A microcomputer program for hydropathic analysis of proteins with I/O through word processing and graphics software.

A BASIC program has been devised for the hydropathic analysis of protein sequences according to the method of Kyte and Doolittle (1982). The program uses sequence data from input files that are created with a word processor and produces two types of output file: one contains a bar graph of the hydropathic profile in a format that can be easily edited; the other is a tabulation of hydropathic indices along a protein's sequence that can be used as input by the program for the production of a bar graph or as input into other graphics and analysis software. An MS-DOS microcomputer, operating under IBM BASICA or GWBASIC and a dot matrix printer with block graphics capabilities are the only hardware requirements for graphic display of hydropathy profiles. The program is capable of unattended analysis from a list of up to 15 input files.

Amino Acid Sequence↗

PubMed1986

A software package for the manipulation, display and analysis of electron and light microscope data.

Quantitative light and electron microscopy is an expanding field which has found applications in many biological disciplines. Computer-enhanced data-acquisition has led to increased speed and accuracy, and combined with computational analysis, stereological parameters can be quickly derived and spatial hypotheses can be easily tested. A software package is described, which controls the manipulation, display and analysis of two-dimensional microscope data. Features include alignment of specimens, rotations, translations, deletions, recoding, perimeter and area measurement, point-counts, tests of dispersion and tests of spatial distributions. The programme is graphics-orientated and supports various point-plot modes and histograms. It includes linear and non-linear curve-fitting options and has been specifically designed to encourage new analysis procedures, which automatically benefit from existing graphics options.

Data Collection↗

PubMed1986

METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer.

METAMOD, a BBC microcomputer-based software package for steady-state modelling and control analysis of model metabolic pathways, is described, The package consists of two programs. METADEF allows the user to define the pathway in terms of reactions, rate equations and initial concentrations of metabolites. METACAL uses one of two algorithms to calculate the steady-state concentrations and fluxes. One algorithm uses the current ratio of production and consumption rates of variable metabolites to adjust iteratively their concentrations in such a way that they converge towards the steady state. The other algorithm solves the roots of the system equations by means of a quasi-Newtonian procedure. Control analysis allows the calculation of elasticity, control and response coefficients, by means of finite difference approximation. METAMOD is interactive and easy to use, and suitable for teaching and research purposes.

Algorithms↗

PubMed1987

Interfacing similarity search software with the sequence retrieval system ACNUC.

A method of interfacing sequence similarity search software with the fast sequence retrieval system ACNUC is described. The method is written in FORTRAN 77 and is straightforward to implement because no text-processing code is required--a minimum of 12 extra lines of FORTRAN provided the interface for most applications. The method is also efficient, since sequences are located by simple indexing techniques, with no linear searches of large database files necessary.

Algorithms↗

PubMed1990

SIMFIT: a microcomputer software-toolkit for modelistic studies in biochemistry.

A software package suitable for personal computers and designed to handle simulation and fitting problems related to the study of biomolecules under pre-steady and steady state conditions is presented, and its overall architecture as well as the implemented algorithms illustrated. The peculiar features of the package are: (i) integrated capability of simulating dynamic models and fitting to them experimental data; (ii) handling of stiff problems; (iii) free use of algebraic as well as differential equations; (iv) objective comparison of models of different complexity. The above features are discussed through a number of examples taken from the direct experience of the authors in enzyme kinetics and ligand binding.

Biochemical Phenomena↗

PubMed1990

PROLANG: an expandable software in protein chemistry.

PROLANG is an improved version of the PROSOFT program. Improvements to the old commands were made and new ones were added, PROLANG is an open software that users with BASIC programming experience can easily expand.

Chemical Phenomena↗

PubMed1992

Analysis of gene evolution: the software AGE.

The software AGE (Analysis of Gene Evolution) has been developed both to study a genetic reality, i.e. the identification of statistical properties in genes (e.g. periodicities), and to simulate this observed genetic reality, by models of molecular evolution. AGE has two types of models: (i) models of sequence creation from oligonucleotides: concatenation model in series of an oligonucleotide, independent (or Markov) mixing model of oligonucleotides according to given probabilities (or a Markov matrix); (ii) models of sequence evolution from created sequences: insertion/deletion process of (mono,di,tri)nucleotides, base mutation process. The study of a reality and the development of simulation models are based on several new algorithms: approximated simulation and exact calculus to compute various autocorrelation functions, Fourier transformation of autocorrelation curves, recognition of a curve form, etc. AGE is implemented on IBM or compatible microcomputers and can be used by biologists without any computer knowledge to identify statistical properties in their newly determined DNA sequence and to explain them by models of molecular evolution.

Algorithms↗

PubMed1992

CLUSTAL V: improved software for multiple sequence alignment.

The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added. The new software is a single program called CLUSTAL V, which is written in C and can be used on any machine with a standard C compiler. The main new features are the ability to store and reuse old alignments and the ability to calculate phylogenetic trees after alignment. The program is simple to use, completely menu driven and on-line help is provided.

Phylogeny↗

PubMed1993

GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems.

GEPASI is a software system for modelling chemical and biochemical reaction networks on computers running Microsoft Windows. For any system of up to 45 metabolites and 45 reactions, each with any user-defined or one of 35 predefined rate equations, one can produce trajectories of the metabolite concentrations and obtain a steady state (if it does exist). When steady-state solutions are produced, elasticity and control coefficients, as defined in metabolic control analysis, are calculated. GEPASI also allows the automatic generation of a sequence of simulations with different combinations of parameter values, effectively scanning a hyper-solid in parameter space. Together with the ability to produce user-defined columnar data files, these features allow for both very quick and systematic study of biochemical pathway models. The source code (in C) is available on request from the author, and while the user interface is dependent on having MS-Windows as the operating system, the numerical part is portable to other operating systems. GEPASI is suitable both for research and educational purposes. Although GEPASI was written with biochemical pathways in mind, it can equally be used to stimulate other dynamical systems.

Algorithms↗