Multiple sequence alignment: STRAP

Author: Christoph Gille
Institut für Biochemie, Charité
Humboldt-Universität zu Berlin
Group for Computational Biochemistry
Group Leader: Prof. H. Holzhütter
www.charite.de/sysbio/

Interactive
Structure based
Sequences Alignment Program
STRAP

The free computer program STRAP aligns proteins by sequence and 3D-structure. It 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.

Import and export of proteins is very easy by Drag-and-Drop. The alignment can be exported and modified in MS-Word or other text processors (Example). 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 STRAP software is programmed in Java and runs on all platforms. It has been developed under Linux and optimized for Macintosh OSX. STRAP will be permanently improved.

**Protein superposition** of four proteins.

Convenient Web-Start

Java version 1.5 or higher is needed. To start STRAP click the "Launch"-button in the navigation panel which links the file strap.jnlp. The size of STRAP is 3 MByte.

Depending on the configuration of the Web-Browser, it may not work. Click here if you encounter problems with Java-Webstart.

Manual Installation and Deinstallation

Jar-file: strap.jar

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 alter the Windows-Registry and does not add or modify global configuration files. All files reside in ~/.StrapAlign/ (on Windows C:\StrapAlign\).

PDF-output of a **multiple alignment** in hydropathy shading. Above the alignment the secondary structure is drawn. Below the alignment, arrows point at functionally important positions. Strap uses TeXshade for PDF export.

Documentation

Manual (HTML)
Tutorials are found in [menu-bar > Tutorials] in STRAP

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

Loading and saving of proteins is very important. The following three movies demonstrate, how is used for proteins in STRAP.
- Loading proteins from the file system (0.1 MByte)
- Loading proteins from Web resources - Example Uniprot (1 MByte)
- Loading proteins from Web resources - Example PDB (0.2 MByte)
- Copying proteins to the file system.(0.1 MByte)
- Context menus.(0.1 MByte)
With STRAP you can handle 3D-structures. This is demonstrated in the following flash movies
- Showing residue selections in 3D

Previous program versions are found in the Archive

Main features of STRAP

Computation of sequence alignments (Align-m, Amap, ClustalW-2.0.10, Dialign, Dialign-T, JAligner, Kalign, Mafft, Muscle Neobio, ProbCons, T_coffee)
Computation of 3D-superpositions (Example output) and structure based multiple alignments of proteins with TM-align or CE or Gangsta+ 3D-superposition. Combined sequence-structure alignments.
3D-visualization using OpenAstexViewer or Pymol or Jmol or Rasmol and VMD. In preparation: yasara Highlighting mutations, SNPs, exon-intron boundaries or regions with high sequence conservation in 3D. Instant cross-selection between 3D objects, sequences and alignments
Blast search including "Blast Alert"
Prediction:Transmembrane helices, Secondary Structures and Coiled-Coil
Translation of nucleotide sequences to amino acid sequences. Output of amino acid alignments as nucleotide alignments.
Protein file formats: Swissprot, PDB, Fasta, MSF, Stockholm, Clustalw, Nexus, HSSP Genbank, EMBL
Phylogenetic trees with ATV, Jalview and GeneBee
Residue annotations and nucleotide annotations
Highlighting regular expressions (i.e. Prosite-Patterns) using Incremental search and sequence features from BioDAS servers
Aiding tricky sequence alignments due to low sequence similarity by:
- 3D-superposition of C-alpha atoms using and to highlight spatial equivalent residues
- Dotplot
- Intermediate Sequences
- Mixed sequence alignments and protein structure alignments
Plugins are extensions for STRAP from third-party developers.

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.

Alignment Export

The sequence alignment can be exported in various formats:

Plain text output formats are Clustalw, MSF, HSSP and multiple Fasta. Optionally, the coding nt-sequence can be displayed together with amino acid sequences (Example)
In HTML (Example)
In an MS-Word and OpenOffice complient HTML format. This allows manual modification of the alignment.
In PDF format. Different color schemes are available such as Conservation and Hydropathy. A Fingerprint gives an overview over the alignment. The PDF export can contain charts of computed values (Examples: by color and bars). For more details see TeXshade.

Web-links for STRAP

Advanced export functions
including PDF and Jalview

STRAP provides an easy way to integrate alignments or protein views in web-pages, E-mails and office documents.

Ordinary web-links: A limited amount of information can be packed directly into the web address.
Script commands in Web-pages: For complex tasks the scripting language can be used in in conjunction with web-forms.

Links can be formed automatically using the dialog Menubar>File>Publish alignment For using BioJava together with STRAP please see BioJava.
These techniques are employed by the following web services to use STRAP as a viewer:

The interaction of web pages and STRAP is demonstrated in the Adobe flash animation STRAP web links (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 Drag-And-Drop and the alignment is shown in the web-Browser and in MS-Word.

Tools

Conversion of protein files and alignment file formats:

 java -jar strap.jar -toFasta proteinFile1 proteinFile2 proteinFile3 ...

 java -jar strap.jar -toClustal alignmentFile1 alignmentFile2 alignmentFile3 ...

^{eLearning: eLearning

Alignment projects: See: Alignment Projects

My other software projects: Other software}

News

Nov 2005: BTI contact. Improving GUI
Jan 2008: Jalview interface added
Jul 2008: Serialization of alignments in Web-links
Mar 2009: BioDAS servers for Sequence features
Mar 2009: New 3D-Superposition Program: Gangsta+
Jan 2010: OpenAstexVieweradded
Mai 2010: Creation of a lite version. Tighter integration into Metannogen

Bug reports and suggestions to christoph.gille

charite.de
If you are frustrated because a previously working feature is broken then use a Previous version or Previous version before 2010 from the archive and report the bug.

Convenient Web-Startwiki('Java_web_start')