Sequence Alignment Homework Clip


A ready-to-use Strap installation exists in the Charite network.

Above installation methods will not work on Charite leasing PCs without administrator privileges.
This is because current Java and standard web browsers cannot be installed.


To run Strap on Windows PCs in the Charite, simply download Charite_Strap.bat to the Desktop or any other directory.
For Internet Explorer right-click the link to open its context menu.
In the context menu activate Ziel speichern unter ....

Then double click the downloaded batch file Charite_Strap.bat.

Running for the 1st time, Java 1.8 is installed. Unless Strap is up-to-date, it will be downloaded.
It takes some minutes, before Strap is started. Please confirm the disclaimer message.

At the top of the Strap Program you find a button to install Cygwin.
Most users will need Cygwin. In the Cygwin installation window, please confirm everything. When it asks for a mirror, please select one ending with de for Deutschland. Installation of Cygwin will take ~ 10 minutes. Then, Strap is ready to use. When certain modules are used for the first time, they will be downloaded and compiled. This may also take a few minutes.
Do not hesitate to ask for help, report problems or request new features. Phone 528045 or
christoph.gillecharite.de




Utilities
  • Iridiumbrowser   Unfortunately, Internet Explorer discontinued support for drag-and-drop.
    Drag-and-drop facilitates Loading sequences from the web.
    Iridium is a fast full featured web browser which can be used as a workaround.
    You will find an alias on the desktop and in the directory containing the bat-file.
  • AlwaysOnTopMaker.exe   Sometimes, for simplifying the operate, you need to make an application on top of other applications.
    In these conditions, you need Always On Top Maker, it is a tiny tool to make a window "always on top (TOPMOST)".
    Once Always On Top Maker is initialized, you can use the Ctrl+Alt+T key combination to make a window
    stay on top of other frames or make a topmost window not always on top.
  • Java Runtime Environment (JRE) The Java installation of Charite standard PCs is out of date and most Java software won't run.
    The Java installed here can be used to run other Software.
    The directory, where it is installed can be obtained from the Script text of the Batch file.
Disclaimer. No warranty that installation tools, Iridiumbrowser, AlwaysOnTopMaker, Java embedded programs for alignment computation, structure prediction, 3D-visualization and Strap itself will be free from harmful code, so-called Malware. If you worry about safety, consider using a Virtual Machine or a Sandbox.

On Apple Macintosh OS, menu-bars are located at the top of the screen.
Strap can run in screen menu-bar mode:
Activation: Download Strap and edit strap.command: Directly after the java command add -Dapple.laf.useScreenMenuBar=true .
Limitations: Menu icons will not be shown. Menu items cannot be undocked.

News:

  • Browser based Web application for desktop PCs and tablet computers (iOS, Andreoid, MS-Mobile) which runs entirely without Java.
    Please cite: Alignment-Annotator web server: rendering and annotating sequence alignments (2014) Nucleic Acids Res
  • Strap runs on Windows 10.
  • Feb-2018 new version fixes problems caused by changes of external web services like EBI.
With this free Java software you can:
  • Use latest bioinformatics tools with an intuitive user interface
  • Compare proteins by sequence and 3D-similarity
  • Search protein databases
  • Underline important sequence positions e.g. phosphorylated or glycosylated residues
  • Predict secondary structure, Transmembrane helices and Coiled Coil
  • Create high quality figures for publications with PDF (Example), MS-Word (Example), Libre Office, Open Office and Gwrite
  • Export to MSF, Clustal, HSSP, Multiple Fasta and Jalview
  • Publish interactive protein alignments online with HTML5
More ...






Author: christoph.gillecharite.de
Institut für Biochemie, Charité Berlin


Tested platforms:
Windows XP, Windows 7, Windows 8, Windows 10, Mac OS X 1.5 Leopard (PPC), Mac OS X 1.6 Snow Leopard, Apple OS X Lion, Linux, Solaris, Open Solaris

The Security concepts prevents damage of data and protects the user's privacy.

Смотрите, полоска осталась незагорелой. Похоже, он носил кольцо. Офицер был поражен этим открытием. - Кольцо? - Он вдруг забеспокоился. Вгляделся в полоску на пальце и пристыжено покраснел.

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