msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design

msatcommander is a platform-independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated, fasta-formatted files. Search data and locus-specific primers are written to comma-separated value files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports at least Python 2.4, Biopython 1.43, and wxPython 2.8. msatcommander is available from http://code.google.com/p/msatcommander/.     

MICROSATELIGHT--pipeline to expedite microsatellite analysis

MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy-Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/.     

TRITON: in silico construction of protein mutants and prediction of their activities

MOTIVATION: One of the objectives of protein engineering is to propose and construct modified proteins with improved activity for the substrate of interest. Systematic computational investigation of many protein variants requires the preparation and handling of a large number of data files. The type of the data generated during the modelling of protein variants and the estimation of their activities offers the possibility of process automatization. RESULTS: The graphical program TRITON has been developed for modelling protein mutants and assessment of their activities. Protein mutants are modelled from the wild type structure by homology modelling using the external program MODELLER. Chemical reactions taking place in the mutants active site are modelled using the semi-empirical quantum mechanic program MOPAC. Semi-quantitative predictions of mutants activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of active site residues during the reaction. The program TRITON offers graphical tools for the preparation of the input data files, for calculation and for the analysis of the generated output data. AVAILABILITY: The program TRITON can run under operating systems IRIX, Linux and NetBSD. The software is available at http://www.chemi.muni.cz/lbsd/triton.ht ml.     

An algorithm of step-by-step pedigree drawing

An algorithm for drawing large, complex pedigrees containing inbred loops and multiple-mate families is presented. The algorithm is based on a step-by-step approach to imaging, when the researcher determines the direction of further extension of the scheme. The algorithm is implemented as the PedigreeQuery software package written in Java. The software has a convenient graphical interface. The software package permits constructing not only whole pedigrees, but also their fragments that are particularly interesting for research. It also allows for adding new information on the phenotypes and genotypes of pedigree members. PedigreeQuery is distributed free of charge; it is available at http://mga.bionet.msc.ru/PedigreeQuery/PedigreeQuery.html and ftp://mga.bionet.msc.ru/PedigreeQuery/.     

An Algorithm of Step-by-step Pedigree Drawing

An algorithm for drawing large, complex pedigrees containing inbred loops and multiple-mate families is presented. The algorithm is based on a step-by-step approach to imaging, when the researcher determines the direction of further extension of the scheme. The algorithm is implemented as the PedigreeQuery software package written in Java. The software has a convenient graphical interface. The software package permits constructing not only whole pedigrees, but also their fragments that are particularly interesting for research. It also allows for adding new information on the phenotypes and genotypes of pedigree members. PedigreeQuery is distributed free of charge; it is available at http://mga.bionet.msc.ru/PedigreeQuery/PedigreeQuery.html and ftp://mga.bionet.nsc.ru/PedigreeQuery/.     

GradientOptimizer: An open‐source graphical environment for calculating optimized gradients in reversed‐phase liquid chromatography

We here present GradientOptimizer, an intuitive, lightweight graphical user interface to design nonlinear gradients for separation of peptides by reversed‐phase liquid chromatography. The software allows to calculate three types of nonlinear gradients, each of them optimizing a certain retention time distribution of interest. GradientOptimizer is straightforward to use, requires minimum processing of the input files, and is supported under Windows, Linux, and OS X platforms. The software is open‐source and can be downloaded under an Apache 2.0 license at https://github.com/statisticalbiotechnology/NonlinearGradientsUI .     

Excel2SVM: a stand-alone Python tool for data analysis via support vector machines

The creation of classification kernel models to categorize unknown data samples of massive magnitude is an extremely advantageous tool for the scientific community. Excel2SVM, a stand-alone Python mathematical analysis tool, bridges the gap between researchers and computer science to create a simple graphical user interface that allows users to examine data and perform maximal margin classification. This valuable ability to train support vector machines and classify unknown data files is harnessed in this fast and efficient software, granting researchers full access to this complicated, high-level algorithm. Excel2SVM offers the ability to convert data to the proper sparse format while performing a variety of kernel functions along with cost factors/modes, grids, crossvalidation, and several other functions. This program functions with any type of quantitative data making Excel2SVM the ideal tool for analyzing a wide variety of input. The software is free and available at www.bioinformatics.org/excel2svm. A link to the software may also be found at www.kernel-machines.org. This software provides a useful graphical user interface that has proven to provide kernel models with accurate results and data classification through a decision boundary.     

A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies

THESIAS (Testing Haplotype EffectS In Association Studies) is a popular software for carrying haplotype association analysis in unrelated individuals. In addition to the command line interface, a graphical JAVA interface is now proposed allowing one to run THESIAS in a user-friendly manner. Besides, new functionalities have been added to THESIAS including the possibility to analyze polychotomous phenotype and X-linked polymorphisms. AVAILABILITY: The software package including documentation and example data files is freely available at http://genecanvas.ecgene.net. The source codes are also available upon request.     

Bosque: integrated phylogenetic analysis software

Phylogenetic analyses today involve dealing with computer files in different formats and often several computer programs. Although some widely used applications have integrated important functionalities for such analyses, they still work with local resources only: input/output files (users have to manage them) and local computing (users have sometimes to leave their programs, on their desktop computers, running for extended periods of time). To address these problems we have developed 'Bosque', a multi-platform client-server software that performs standard phylogenetic tasks either locally or remotely on servers, and integrates the results on a local relational database. Bosque performs sequence alignments and graphical visualization and editing of trees, thus providing a powerful environment that integrates all the steps of phylogenetic analyses. AVAILABILITY: http://bosque.udec.cl     

StructureSelector: A web‐based software to select and visualize the optimal number of clusters using multiple methods

Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program structure has been widely used to infer population genetic structure. However, previous studies demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure. The most widely used ΔK method tends to identify the uppermost hierarchy of population structure. Recently, four alternative statistics (medmedk , medmeak , maxmedk and maxmeak ) were proposed, which appear to be more accurate than the previously used methods for both even and uneven sampling data. However, the lack of easy‐to‐use software limits the use of these appealing new estimators. Here, we developed a web‐based user‐friendly software structureselector to calculate the four appealing alternative statistics together with the commonly used Ln Pr(X|K) and ΔK statistics. structureselector accepts the result files of structure , admixture or faststructure as input files. It reports the “best” K for each estimator, and the results are available as HTML or tab separated tables. The program can also generate graphical representations for specific K, which can be easily downloaded from the server. The software is freely available at http://lmme.qdio.ac.cn/StructureSelector/ .     

IPeak: An open source tool to combine results from multiple MS/MS search engines

Liquid chromatography coupled tandem mass spectrometry (LC‐MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post‐processing algorithm and multi‐search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command‐line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml‐lib/ .     

SeqTrace: A Graphical Tool for Rapidly Processing DNA Sequencing Chromatograms

Modern applications of Sanger DNA sequencing often require converting a large number of chromatogram trace files into high-quality DNA sequences for downstream analyses. Relatively few nonproprietary software tools are available to assist with this process. SeqTrace is a new, free, and open-source software application that is designed to automate the entire workflow by facilitating easy batch processing of large numbers of trace files. SeqTrace can identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and end-trim finished sequences. The software features a graphical interface that includes a full-featured chromatogram viewer and sequence editor. SeqTrace runs on most popular operating systems and is freely available, along with supporting documentation, at http://seqtrace.googlecode.com/.     

BioDownloader: bioinformatics downloads and updates in a few clicks

There are many ftp or http servers storing data required for biological research. While some download applications are available, there is no user-friendly download application with a graphical interface specifically designed and adapted to meet the requirements of bioinformatics. BioDownloader is a program for downloading and updating files from ftp and http servers. It is optimized to work robustly with large numbers of files. It allows the selective retrieval of only the required files (batch downloads, multiple file masks, ls-lR file parsing, recursive search, recent updates, etc.). BioDownloader has a built-in repository containing the settings for common bioinformatics file-synchronization needs, including the Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI) databases. It can post-process downloaded files, including archive extraction and file conversions. AVAILABILITY: The program can be installed from http://dunbrack.fccc.edu/BioDownloader. The software is freely available for both non-commercial and commercial users under the BSD license.     

GoSurfer

The analysis of complex patterns of gene regulation is central to understanding the biology of cells, tissues and organisms. Patterns of gene regulation pertaining to specific biological processes can be revealed by a variety of experimental strategies, particularly microarrays and other highly parallel methods, which generate large datasets linking many genes. Although methods for detecting gene expression have improved substantially in recent years, understanding the physiological implications of complex patterns in gene expression data is a major challenge. This article presents GoSurfer, an easy-to-use graphical exploration tool with built-in statistical features that allow a rapid assessment of the biological functions represented in large gene sets. GoSurfer takes one or two list(s) of gene identifiers (Affymetrix probe set ID) as input and retrieves all the Gene Ontology (GO) terms associated with the input genes. GoSurfer visualises these GO terms in a hierarchical tree format. With GoSurfer, users can perform statistical tests to search for the GO terms that are enriched in the annotations of the input genes. These GO terms can be highlighted on the GO tree. Users can manipulate the GO tree in various ways and interactively query the genes associated with any GO term. The user-generated graphics can be saved as graphics files, and all the GO information related to the input genes can be exported as text files. AVAILABILITY: GoSurfer is a Windows-based program freely available for noncommercial use and can be downloaded at http://www.gosurfer.org. Datasets used to construct the trees shown in the figures in this article are available at http://www.gosurfer.org/download/GoSurfer.zip.     

PrepMS: TOF MS data graphical preprocessing tool

We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings, experimentally determined to work well in most situations. These values, if desired, can be changed by the user. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection and visual data quality assessment. AVAILABILITY: Stand-alone executable files and Matlab toolbox are available for download at: http://sourceforge.net/projects/prepms     

BACA: a mitochondrial genome retriever,organizer and visualizer

Retrieving and organizing data from complete genomes is a time‐consuming task, even more so if the interest lies only in part of the genome (for nongenomic analysis). Furthermore, when comparing several genomes or genes, data retrieval has to be repeated multiple times. We present baca , a software for retrieving, organizing and visualizing multiple mitochondrial genomes. baca takes a GenBank query, retrieves all related genomes and generates multiple fasta files organized both by genomes and genes. A web‐based user interface and an interactive graphical map of all genomes with all genes are also provided. The program is available from http://cibio.up.pt/software/baca .     

FitDockApp：基于模板的分子对接PyMOL插件图形化计算软件

目的 分子对接在预测分子之间的结合模式和亲和力方面起着至关重要的作用,是计算结构生物学和计算机辅助药物设计研究的重要方法。本研究团队近期开发了一款基于模板的新型对接方法FitDock,当存在近似的蛋白质配体模板时,它在准确性和速度方面都超过了业界常用的分子对接方法。为了增强FitDock方法的可用性,使其在分子模拟领域得到更广泛的应用,很有必要发展图像化的软件工具。方法 基于Python图像化编程,本文开发了FitDockApp,这是分子可视化软件PyMOL的插件软件。结果 FitDockApp能够通过操作窗口界面,实现基于模板的分子对接和配体结构比对,实时显示预测三维结构,并提供将对接文件上传到实验室服务器获取最优模板的便利。此外,FitDockApp还具备批量对接功能。结论 FitDockApp通过用户友好的界面简化了对接过程,并提供丰富的功能,帮助研究人员获得精确的对接结果。FitDockApp是一款免费软件,兼容Windows和Linux系统,可在http://cao.labshare.cn/fitdock/下载。     

一个可用于复杂大群体的可视化系谱绘制和分析软件

对于在遗传研究和家系研究中大的系谱结构图还很难分析。系谱的绘制通常是遗传性状的分析研究的第一步。系图可以反映整个群体的结构、每个个体之间的相互关系以及基因流的走向,便于理解遗传性状的本质。因为所用家系数目的增大和复杂性的增加,绘制1个清晰的系谱有时变得十分困难。因此开发了1种名为Pedigraph软件,可以解决这个问题。Pedigraph能够完成对于大的复杂的群体的系谱绘制工作,并能进行相应的系谱分析。初步的测试表明这个软件在研究动植物的遗传育种中是1个有用的工具,同时它也可以用于人类的群体和历史等方面的研究。     

An integrated system for high throughput TaqMan based SNP genotyping.

We have developed an integrated laboratory information system that allows the flexible handling of pedigree, phenotype and genotype information. Specifically, it includes client applications for an integrated data import from TaqMan typing files, Mendel checking, data export, handling of pedigree and phenotype information and analysis features. AVAILABILITY: The SQL source code, sources and binaries of the client applications (NT and Windows95/98 platforms) and additional documentation are available at http://www.mucosa.de/.