Click to start Strap
launch


Author: Christoph Gille
Institut für Biochemie, Charité Berlin
@ christophgil @ googlemail .com



Interactive
Structure based
Sequences Alignment Program
Strap

The free computer program Strap aligns proteins by sequence and 3D-structure und Windows, Macintosh, Linux and Unix. Run the demo showing 6 sequences of the proteasome within a Strap session.

Secure Strap session
Strap requires Java. In all versions of Strap, modifying file operations are strictly checked to prevent damage of data on the computer. The Strap "Lite" version used for above demo has additional restrictictions to improve security: It does not have permission to run external programs nor to load further Java code.

After starting the demo you will see 6 amino acid sequences. For three of them the 3D-structure is known. Those are well superimposed in 3D even though the similarity is hardly recognized at sequence level. Some important positions are marked in the sequence. These underlinings might be dragged into the 3D-view.




Strap supports the simultaneous analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence and residue annotation.
Snapshot of the Strap application. Bottom panel: Multiple sequence alignment in Strap. Four proteins are selected and conserved amino acids are colorized according to chemical property. Top panel: One of the proteins is shown in 3D.
screenshot
The alignment can be exported and modified in MS-Word or other text processors. Import and export of proteins is very easy by . The included tutorial will teach the use of Strap in as little as one hour. The scriptability and extendability make Strap a very powerful tool for even the most advanced users. The software programmed in Java and runs on all platforms. It will be permanently improved.
Protein superposition of four proteins.
superposition

Getting started - run demo

Click to run demo An alignment of orthologous and paralogous sequences of the core of the proteasome is shown. Each alignment row contains the amino acid sequence and the row header with the sequence name. The row headers have a context menu (right click) and can be moved/copied with the mouse (so-called ).

Important sequence positions are highlighted after some time. A detailed balloon message appears when the mouse pointer is over the underlining. The information is freshly downloaded from various servers in the world and will be up-to-date which causes a delay of a few moments. They have a context menu (right click), they can be selected by Ctrl+click and can be copied by .

The 3D-structures are not directly available. This is because only sequence information is primarily present. Nevertheless, homologous 3D-models can be inferred using the tool-button "3D". This automated search for homologous structures is based on an up-to-date copy of the structure database. After association of 3D-coordinates from an homologous entry from the protein structure database, the structure can be viewed.
For those who are rather careful with unknown software: If you do not yet trust Strap completely, run the light version with restricted permissions - hence higher security. Strap will not permit native code to be executed and will not load further java code. Also see "Security" in the navigation panel. Run light version


Web-Start

Java is needed. Click the "Launch"-button in the navigation panel which links the file strap.jnlp.

Depending on the configuration of the Web-Browser, it may not work: In case of problems.

OutOfMemoryError

By default, Strap must not use more than 250 MByte. Therefore, Strap may throw an OutOfMemoryError. Here you can start Strap with more memory.
Memory=MBytes
OutOfMemoryError often occurs with the 3D-superposition method CE for very large proteins. Solution: The method TM_align requires less memory. The superposition method can be changed with the context menu of the align-tool-button (right click) or in the Superposition menu of the 3D-view.

The amount of free memory can be monitored in Strap in the left side pane which need to be opened with the mouse first.

Also see
What_is_heap_size_in_Java

Manual Installation and Deinstallation

:
strap.jar (3.3 MByte)
Install manually if Web-start failed: Download strap.jar (3 MByte) and double click or type the command line: java -jar strap.jar

Uninstall: Strap does not change the system. It does not modify global configuration files . All files reside in .

Previous program versions are found in the Archive or Archive before 2010
PDF-output of a multiple alignment in hydropathy shading. Above the alignment the is drawn. Below the alignment, arrows point at functionally important positions. Strap uses TeXshade for PDF export.
protein  alignment

Documentation

The movies can be watched with an -player. Please install adobe-flashplugin. Each movie takes about 1 to 3 min.

Main features of Strap

DNA translated to amino acids. Three (not necessarily consecutive) nucleotides form a triplet and code for one amino acid. Exons are black and introns gray. Thre amino acids are highlighted with a green background. The view is synchronized with the alignment view.
screenshot

Alignment Export

The sequence alignment can be exported in various formats:

Strap in Web-pages

Advanced export functions
including PDF and Jalview
superposition
Strap provides an easy way to integrate alignments or protein views in web-pages, E-mails and office documents.
  1. Web-variables: A limited amount of information can be passed as web-variables in the address.
  2. Script commands: For complex tasks the scripting language can be used in the web page.
Links can be formed automatically using the dialog Menubar>File>Export Alignment>Publish alignment

Strap is used as a viewer by:
The interaction of web pages and Strap is demonstrated in the animation movie (1.1 MByte). Strap with reduced functionality ( invisible menu-bar) serves as a simple web-viewer for proteins. Static web links are clicked by the user to load proteins. In the video four pdb files are loaded and structurally aligned. The files are saved on the desktop by and the alignment is shown in the web-Browser and in MS-Word.

eLearning

Strap has been used for blended eLearning in various modelling courses in the world. It will be used as an eLearning tool for students of human medicine. First results can be seen here: eLearning

News



Bug reports and suggestions to
@ christophgil @ googlemail .com

If a previously working feature is broken then use a Previous version and report the bug.