Chimera: construction of chimeric sequences for phylogenetic analysis

SUMMARY: Chimera allows the construction of chimeric protein or nucleic acid sequence files by concatenating sequences from two or more sequence files in PHYLIP formats. It allows the user to interactively select genes and species from the input files. The concatenated result is stored to one single output file in PHYLIP or NEXUS formats. AVAILABILITY: The computer program, including supporting files and example files, is available from http://www.dalicon.com/chimera/.     

MacMolecular: A program for visualization of molecular structures on the Macintosh

MacMolecular displays small- to medium-sized biomolecules, with particular emphasis on peptides. It has been developed to run on color Macintosh computers. The display can be stick, ball and stick, depth cued by thickness stick, or several types of space-filling representations. The program takes input from standard PDB files, simple Cartesian coordinate files, and, in addition, from Kinemage files in which atom information has been included. The program allows color changes of various types as well as the normal functions of translation, rotation, and zooming. In addition, animation files may be produced for subsequent display. Bonding of atoms is done by a distance algorithm (standard) or sequentially to properly display Cα traces and traces of peptides containing simplified representations of amino acids. Stereo viewing is available, and manipulated structures which were drawn from PDB files can be written out to new PDB files. In addition, PICT files of the drawing window can be generated.     

SPIRE: the SPIDER reconstruction engine

SPIRE is a Python program written to modernize the user interaction with SPIDER, the image processing system for electron microscopical reconstruction projects. SPIRE provides a graphical user interface (GUI) to SPIDER for executing batch files of SPIDER commands. It also lets users quickly view the status of a project by showing the last batch files that were run, as well as the data files that were generated. SPIRE handles the flexibility of the SPIDER programming environment through configuration files: XML-tagged documents that describe the batch files, directory trees, and presentation of the GUI for a given type of reconstruction project. It also provides the capability to connect to a laboratory database, for downloading parameters required by batch files at the start of a project, and uploading reconstruction results at the end of a project.     

Formats of image data files that can be used for routine digital light micrography. Part one

Failing to open computer files that describe image data is not the most frustrating experience that the user of a computer can suffer, but it is high on list of possible aggravations. To ameliorate this, the structure of uncompressed image data files is described here. The various ways in which information that describes a picture can be recorded are related, and a primary distinction between raster or bitmap based and vector or object based image data files is drawn. Bitmap based image data files are the more useful of the two formats for recording complicated images such as digital light micrographs, whereas object based files are better for recording illustrations and cartoons. Computer software for opening a very large variety of different formats of digital image data is recommended, and if these fail, ways are described for opening bitmap based digital image data files whose format is unknown.     

Formats of image data files that can be used for routine digital light micrography. Part one

Failing to open computer files that describe image data is not the most frustrating experience that the user of a computer can suffer, but it is high on list of possible aggravations. To ameliorate this, the structure of uncompressed image data files is described here. The various ways in which information that describes a picture can be recorded are related, and a primary distinction between raster or bitmap based and vector or object based image data files is drawn. Bitmap based image data files are the more useful of the two formats for recording complicated images such as digital light micrographs, whereas object based files are better for recording illustrations and cartoons. Computer software for opening a very large variety of different formats of digital image data is recommended, and if these fail, ways are described for opening bitmap based digital image data files whose format is unknown.     

Microarray data assembler

SUMMARY: Large volumes of microarray data are generated and deposited in public databases. Most of this data is in the form of tab-delimited text files or Excel spreadsheets. Combining data from several of these files to reanalyze these data sets is time consuming. Microarray Data Assembler is specifically designed to simplify this task. The program can list files and data sources, convert selected text files into Excel files and assemble data across multiple Excel worksheets and workbooks. This program thus makes data assembling easy, saves time and helps avoid manual error. AVAILABILITY: The program is freely available for non-profit use, via email request from the author, after signing a Material Transfer Agreement with Johns Hopkins University.     

Formats of image data files that can be used in routine digital light micrography. Part two

This is part two of an article that describes the properties of the image data files that are encountered routinely in digital light micrography. In the current part of the article, the differences between saving image data as large intact files and smaller files that have had some information removed, i.e., using lossy compression, are related first. Subsequently, appropriate ways of configuring computers to deal with the large intact image data files are suggested. The structures of the image data files used for recording dynamic sequences and kinematic animations of series of digital light micrographs, i.e., movie formats, are then described. Finally, some information is supplied about choosing file formats for compressing both static and dynamic image data sets.     

Formats of image data files that can be used in routine digital light micrography. Part two

This is part two of an article that describes the properties of the image data files that are encountered routinely in digital light micrography. In the current part of the article, the differences between saving image data as large intact files and smaller files that have had some information removed, i.e., using lossy compression, are related first. Subsequently, appropriate ways of configuring computers to deal with the large intact image data files are suggested. The structures of the image data files used for recording dynamic sequences and kinematic animations of series of digital light micrographs, i.e., movie formats, are then described. Finally, some information is supplied about choosing file formats for compressing both static and dynamic image data sets.     

Assemblages et chaînages de fichiers cartes dans un système automatisé: Une application en paléontologie

enThe storage of taxonomical, stratigraphical, geographicaland bibliographical data, some being coded, about ammonites from Upper Jurassic has begun since 1972 and constituts three files with punch-cards: types, citations and synonymies. The disappearing of punch-cards leads to the making of a system with software allowing the combination and the chaining of files. The combination allows the gathering of data from different files and the chaining, thanks to decoding files the translation in clear of coded data.Simplicity in the procedures, swiftness in the execution and printing in clear are the principal advantages of the use of the software Texto.     

机用ProTaper 进行恒磨牙根管预备的临床评价

目的:评价机用ProTaper镍钛根管器械进行恒磨牙根管预备的临床疗效。方法:2007年7月至2010年12月期间就诊的需进行根管治疗的109患者,共计128颗磨牙,包括牙髓炎54颗牙,慢性根尖周炎74颗牙。按随机配对原则分入实验组和对照组,每组64颗牙。实验组用机用ProTaper镍钛根管锉预备根管,对照组用不锈钢K型锉预备根管。两组均采用侧向加压法充填根管,记录每颗患牙的单个根管预备所用时间、根管充填效果、术后不良反应及随访到的远期疗效。结果:机用ProTaper镍钛器械预备单根管所耗时间明显少于对照组,根管预备后疼痛发生率明显低于对照组,根管适充率实验组明显优于对照组,根管治疗术后1年疗效比较也优于对照组。结论:使用机用ProTaper器械进行恒磨牙根管预备快速有效,根充效果好,并发症发生率低,远期疗效确切,值得临床推广。     

GenoProfiler: batch processing of high-throughput capillary fingerprinting data

High-throughput content fingerprinting techniques employing capillary electrophoresis place new demands on the editing of fingerprint files for the downstream contig assembly program, FPC. A cross-platform software application, GenoProfiler, was developed for automated editing of sized fingerprinting profiles generated by the ABI Genetic Analyzers. The batch-processing module extracts the sized fragment information directly from the ABI raw trace files, or from data files exported from GeneMapper or other size calling software, removes the background noise and undesired fragments, and generates fragment size files compatible with the FPC software. AVAILABILITY: http://wheat.pw.usda.gov/PhysicalMapping/     

Early ontogeny of vascular cambium

Observations were made on structural changes of procambium and the subsequent appearance of cambium in the developing shoot. The procambium in early stages shows radial seriation of cells as a result of repeated tangential divisions. In tangential view the procambium has initially a rather homogeneous structure and later becomes organized into two distinct systems, one composed of long cells and the other of short cells. The latter cells are arranged tangentially in axial files and transversely in radial files. They show repeated transverse divisions. Some of the short cells elongate to intrude between neighboring cells. Therefore, long cells may be derived both from cells of homogeneous structure in the first stage and from elongation of some of the short cells in axial files. Long cells have mostly tapering end walls and elongate actively. In the subsequent stages, the frequency of transverse divisions of short cells in axial files decreases and these cells expand radially. Short cells in axial files are separated from one another vertically by the elongation of neighboring long cells which break up the axial files as seen in tangential view. The vascular meristem in this stage is believed to initiate the cambium. Eventually, short cells remain mostly single, or form files of two or three cells in height in tangential view. The observations are discussed in relation to the structure of the vascular meristem in other plants.     

concatenator: sequence data matrices handling made easy

concatenator is a simple and user-friendly software that implements two very useful functions for phylogenetics data analysis. It concatenates NEXUS files of several fragments in a single NEXUS file ready to be used in phylogenetics software, such as paup and mrbayes and it converts FASTA sequence data files to NEXUS and vice-versa. Additionally, concatenated files can be prepared for partition tests in paup. It is freely available in http://cobig2.fc.ul.pt.     

TMCompare: transmembrane region sequence and structure.

TMCompare is an alignment and visualization tool for comparison of sequence information for membrane proteins contained in SWISS-PROT entries, with structural information contained in PDB files. The program can be used for: detection of breaks in alpha helical structure of transmembrane regions; examination of differences in coverage between PDB and SWISS-PROT files; examination of annotation differences between PDB files and associated SWISS-PROT files; examination and comparison of assigned PDB alpha helix regions and assigned SWISS-PROT transmembrane regions in linear sequence (one letter code) format; examination of these differences in 3D using the CHIME plugin, allowing; analysis of the alpha and non-alpha content of transmembrane regions. AVAILABILITY: TMCompare is available for use through selection of a query protein via the internet (http://www.membraneproteins.org/TMCompare) CONTACT: tmcompare@membraneproteins.org     

Proteomics FASTA archive and reference resource

A FASTA file archive and reference resource has been added to ProteomeCommons.org. Motivation for this new functionality derives from two primary sources. The first is the recent FASTA standardization work done by the Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI). Second is the general lack of a uniform mechanism to properly cite FASTA files used in a study, and to publicly access such FASTA files post-publication. An extension to the Tranche data sharing network has been developed that includes web-pages, documentation, and tools for facilitating the use of FASTA files. These include conversion to the new HUPO-PSI format, and provisions for both citing and publicly archiving FASTA files. This new resource is available immediately, free of charge, and can be accessed at http://www.proteomecommons.org/data/fasta/. Source-code for related tools is also freely available under the BSD license.     

Lipid Converter,A Framework for Lipid Manipulations in Molecular Dynamics Simulations

Construction of lipid membrane and membrane protein systems for molecular dynamics simulations can be a challenging process. In addition, there are few available tools to extend existing studies by repeating simulations using other force fields and lipid compositions. To facilitate this, we introduce Lipid Converter, a modular Python framework for exchanging force fields and lipid composition in coordinate files obtained from simulations. Force fields and lipids are specified by simple text files, making it easy to introduce support for additional force fields and lipids. The converter produces simulation input files that can be used for structural relaxation of the new membranes.     

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.     

Changes in the pattern of cell arrangement at the surface of the shoot apical meristem in Hedera helix L. following gibberellin treatment

The changes in the pattern of cell arrangement and surface topography at the shoot apical meristem of Hedera helix L., which occur during gibberellic acid (GA₃)-induced transition from spiral to distichous phyllotaxis, were examined by scanning electron microscopy of rapidly frozen tissue. The technique preserves the original shape of the cells in their turgid state. It reveals distinct sets of radially oriented cell files, about four to eight cells wide, which extend from the central region of the meristem toward leaf primordia on the meristem flanks. In apices with spiral phyllotaxis, a new emerging primordium (0) appears as an acropetal bulge between the radial files adjacent to the third (3) and the second (2) older primordia. The bulging is associated with radial or oblique cell divisions while those located at the meristem flanks and in the radial files are oriented tangentially. As the displacement of existing primordia away from the central region increases following the GA₃ treatment, radial and oblique divisions as well as acropetal bulging invade the radial files adjacent to the primordium 2; consequently the angular divergence of the emerging primordium from the youngest existing primordium (1) increases. In apices with distichous phyllotaxis, the earliest bulging appears on both sides of the radial files facing primordium 2, with a slight depression at the files. The radial files therefore correspond to regions of the meristem where acropetal bulging is generally delayed, although this effect apparently diminishes with increasing distance of existing primordia from the meristem center.Abbreviations GA₃ gibberellic acid We thank Mr. Gilbert Ahlstrand, University of Minnesota, for his advice and assistance with the scanning electron microscopy. Contribution of the University of Minnesota Agricultural Experimental Station No. 19032.     

jmzTab: A Java interface to the mzTab data standard

mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab‐delimited file that can capture identification and quantification results coming from MS‐based proteomics and metabolomics approaches. We here present an open‐source Java application programming interface for mzTab called jmzTab. The software allows the efficient processing of mzTab files, providing read and write capabilities, and is designed to be embedded in other software packages. The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table‐based sections in the mzTab files. In this article, as two example implementations, we also describe two stand‐alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab. The library is freely available at http://mztab.googlecode.com .     

EMBLSCAN: fast approximate DNA database searches on compact disc

An algorithm that allows rapid searching of nucleic acid sequencesbased on pregenerated index files is described. The programsand index files for searching the entire EMBL nucleotide sequencecollection are being distributed on the EMBL Data Library^'sCD–ROM.